Contacts of the helix formed by residues 127 - 157 (chain O) 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 O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122O ASP* 5.1 0.2 - - - -
123O HIS* 2.8 20.1 + - - -
124O ALA 5.0 0.2 - - - -
125O ASP 3.5 1.4 - - - -
126O LYS* 1.3 83.3 - - - +
128O ASP* 1.3 68.1 + - - -
129O ALA 3.4 2.2 - - - -
130O LEU 3.5 0.8 + - - -
131O HIS* 3.1 19.8 + - - +
193O LYS* 3.9 15.3 - - - +
197O VAL* 6.5 0.7 - - - -
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Residues in contact with ASP 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O TYR* 4.1 8.9 + - + -
70O PHE* 3.7 16.0 - - + -
75O VAL* 3.6 16.1 - - - +
77O LEU* 3.8 2.6 - - - +
121O PHE 3.5 21.9 - - - +
122O ASP* 3.9 19.0 + - - +
123O HIS 4.3 2.0 - - - +
127O GLY* 1.3 72.4 - - - +
129O ALA* 1.3 76.6 + - - +
131O HIS* 3.4 1.4 + - - +
132O ALA* 2.9 26.7 + - - +
197O VAL* 5.1 0.2 - - - +
190R ARG* 3.3 39.2 + - - -
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Residues in contact with ALA 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O PHE* 4.3 9.4 - - - -
77O LEU* 4.2 8.7 - - + -
80O LEU* 4.6 12.6 - - + +
127O GLY 3.4 0.8 - - - -
128O ASP* 1.3 84.8 + - - +
130O LEU* 1.3 62.4 + - - +
132O ALA* 3.4 2.1 + - - +
133O MET* 3.1 23.9 + - - +
188O LEU* 3.7 18.5 - - + +
197O VAL* 3.7 33.2 - - + -
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Residues in contact with LEU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O LYS* 3.6 35.9 - - + +
127O GLY 3.5 2.2 + - - -
128O ASP 3.4 0.4 - - - -
129O ALA* 1.3 77.6 - - - +
131O HIS* 1.3 59.2 + - - +
133O MET 3.3 1.4 + - - -
134O GLU* 2.9 62.9 + - + +
185O VAL* 3.9 30.1 - - + +
188O LEU* 4.1 19.5 - - + +
189O ARG* 3.9 23.6 - - + +
197O VAL* 5.7 1.7 - - + +
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Residues in contact with HIS 131 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 5.4 12.5 - - + +
118O LEU* 5.9 4.6 - - - +
120O ASP 5.5 0.6 + - - -
121O PHE* 3.4 36.0 - + + +
122O ASP 3.9 9.6 + - - -
123O HIS* 3.4 34.8 + + + -
126O LYS* 4.3 16.1 + - + +
127O GLY 3.1 18.0 + - - +
128O ASP 3.7 2.5 - - - +
130O LEU* 1.3 77.7 - - - +
132O ALA* 1.3 57.4 + - - +
134O GLU* 3.3 4.0 + - - +
135O LEU* 2.9 42.6 + - + +
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Residues in contact with ALA 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O MET* 4.3 7.9 - - - +
70O PHE* 3.4 33.7 - - + -
84O PHE* 4.1 14.9 - - + -
121O PHE* 4.7 9.6 - - + -
128O ASP 2.9 14.2 + - - +
129O ALA 3.8 2.7 - - - +
131O HIS* 1.3 78.7 - - - +
133O MET* 1.3 58.1 + - - +
135O LEU* 3.3 8.2 + - - +
136O ALA* 2.9 28.4 + - - +
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Residues in contact with MET 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80O LEU* 3.3 33.2 - - + -
83O PHE* 4.0 18.8 - - + -
84O PHE* 4.3 6.5 - - - -
129O ALA 3.1 17.0 + - - +
130O LEU* 3.8 3.6 - - - +
132O ALA* 1.3 74.9 - - - +
134O GLU* 1.3 61.0 + - - +
136O ALA* 3.3 2.6 + - - -
137O LEU* 2.9 24.3 + - - +
181O ILE* 3.5 20.0 - - + +
184O TYR* 3.5 51.4 - - + -
185O VAL* 3.8 14.6 - - + +
188O LEU* 3.9 10.8 - - + -
200O PHE* 4.4 5.8 - - + -
204O LEU* 4.1 8.5 - - + -
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Residues in contact with GLU 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.2 8.7 - - + +
28G VAL* 4.4 17.1 - - + +
126O LYS* 2.9 36.5 + - - +
130O LEU* 2.9 41.0 + - + +
131O HIS* 3.8 4.7 - - - +
133O MET* 1.3 73.0 - - - +
135O LEU* 1.3 61.3 + - - +
137O LEU* 3.4 5.2 + - - +
138O SER* 3.0 32.2 + - - -
185O VAL* 4.1 15.3 - - + -
189O ARG* 2.8 35.7 + - - +
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Residues in contact with LEU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G PHE* 3.6 20.0 - - + -
21G VAL* 4.2 22.2 - - + -
25G LEU* 3.7 22.6 - - + +
66O MET* 3.4 26.2 - - + -
118O LEU* 5.1 2.2 - - + -
121O PHE* 3.5 24.9 - - + -
131O HIS* 2.9 29.8 + - + +
132O ALA* 3.5 6.3 - - - +
134O GLU* 1.3 78.4 - - - +
136O ALA* 1.3 56.1 + - - +
138O SER* 3.2 1.9 + - - -
139O LEU* 2.9 32.0 + - + +
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Residues in contact with ALA 136 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O TYR* 3.9 29.2 - - + +
66O MET* 4.6 0.9 - - - +
83O PHE* 5.4 0.4 - - + -
84O PHE* 4.2 13.2 - - + -
132O ALA 2.9 17.4 + - - +
133O MET* 3.6 9.4 - - - +
134O GLU 3.3 0.2 - - - -
135O LEU* 1.3 73.8 - - - +
137O LEU* 1.3 66.0 + - - +
139O LEU* 3.2 4.4 + - - +
140O GLU* 2.9 29.4 + - - +
181O ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G VAL* 4.8 15.7 - - + -
29G PRO* 6.0 0.2 - - + -
36G LEU* 3.8 32.5 - - + +
133O MET 2.9 17.4 + - - +
134O GLU* 3.6 6.3 - - - +
136O ALA* 1.3 76.6 - - - +
138O SER* 1.3 58.4 + - - +
140O GLU* 3.2 3.1 + - + +
141O LYS* 3.0 37.2 + - + +
178O ILE* 3.8 29.2 - - + +
181O ILE* 3.6 11.8 - - + +
182O SER* 3.4 26.9 - - - +
185O VAL* 4.4 14.8 - - + -
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Residues in contact with SER 138 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G VAL* 3.4 22.2 - - - +
24G GLU* 3.7 17.0 - - - +
25G LEU* 3.0 33.6 + - - +
28G VAL* 3.6 10.0 - - - +
134O GLU 3.0 13.9 + - - -
135O LEU 3.2 2.7 + - - -
137O LEU* 1.3 78.2 - - - +
139O LEU* 1.3 56.1 + - - +
141O LYS* 3.3 5.8 + - - +
142O LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE* 5.8 0.2 - - + -
17G PRO* 4.0 27.8 - - + +
18G PHE* 5.5 2.2 - - + -
21G VAL* 4.0 20.0 - - + -
59O VAL* 4.8 16.8 - - + +
62O VAL* 3.7 32.1 - - + -
63O TYR* 4.3 17.5 - - + +
66O MET* 4.0 13.0 - - + -
135O LEU* 2.9 25.3 + - + +
136O ALA* 3.6 4.7 - - - +
138O SER* 1.3 77.2 - - - +
140O GLU* 1.3 58.4 + - - +
142O LEU* 3.4 10.6 + - + +
143O THR* 2.8 32.7 + - - -
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Residues in contact with GLU 140 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O VAL* 4.3 3.6 - - - +
63O TYR* 2.5 32.8 + - - +
91O GLU* 3.7 14.6 - - - +
136O ALA 2.9 21.0 + - - +
137O LEU* 3.7 5.2 - - - +
139O LEU* 1.3 74.1 - - - +
141O LYS* 1.3 61.3 + - - +
143O THR* 3.4 6.6 + - - +
144O ASN* 3.0 17.7 + - - +
174O GLN* 2.6 52.9 + - - +
177O ALA* 4.3 10.2 - - + +
178O ILE* 3.9 16.4 - - + +
181O ILE* 3.5 21.7 - - + +
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Residues in contact with LYS 141 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLU* 3.9 21.9 + - - +
27G LEU 5.7 1.2 + - - -
28G VAL* 6.1 1.7 - - + +
29G PRO* 5.2 8.1 - - - +
35G SER 5.4 0.4 + - - -
36G LEU 2.8 29.7 + - - -
37G ALA* 3.6 16.6 - - - +
38G ARG 3.2 20.2 + - - -
39G GLN* 3.0 46.1 + - + +
137O LEU* 3.0 31.9 + - + +
138O SER* 3.7 5.8 - - - +
140O GLU* 1.3 73.2 - - - +
142O LEU* 1.3 65.8 + - - +
144O ASN* 3.2 1.2 + - - +
145O GLU* 3.0 13.1 + - - +
178O ILE* 4.0 9.9 - - + -
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Residues in contact with LEU 142 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE* 3.4 33.2 - - + -
17G PRO* 4.1 18.2 - - + +
20G GLU* 4.0 33.9 - - + +
21G VAL* 4.5 9.2 - - + +
24G GLU* 4.3 10.2 - - + +
55O VAL* 6.0 0.2 - - + -
59O VAL* 6.4 0.4 - - + -
138O SER 2.9 18.1 + - - +
139O LEU* 3.6 11.9 - - + +
141O LYS* 1.3 76.9 - - - +
143O THR* 1.3 62.7 + - - +
145O GLU* 3.2 20.6 + - - +
146O LYS* 3.0 37.1 + - + +
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Residues in contact with THR 143 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O GLN* 3.9 6.7 - - - +
55O VAL* 4.2 8.9 - - + +
56O GLU* 3.6 31.4 - - - +
59O VAL* 3.5 21.7 - - + +
91O GLU* 5.4 0.2 + - - -
139O LEU 2.8 22.2 + - - -
140O GLU* 3.6 8.1 + - - -
142O LEU* 1.3 76.5 - - - +
144O ASN* 1.3 57.6 + - - +
146O LYS* 3.2 7.3 + - - +
147O LEU* 2.8 36.2 + - + +
174O GLN* 4.0 8.5 - - - +
214O CA 4.2 7.4 - - - -
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Residues in contact with ASN 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 3.0 30.6 + - - +
140O GLU 3.0 13.8 + - - +
141O LYS 3.2 9.4 + - - +
143O THR* 1.3 71.8 - - - +
145O GLU* 1.3 61.0 + - - +
147O LEU* 3.2 2.7 + - - +
148O LEU* 2.9 53.7 + - - +
171O LEU* 4.3 11.4 - - - +
174O GLN* 3.5 30.0 - - + +
175O VAL* 5.1 9.8 - - - +
178O ILE* 3.9 9.0 - - + +
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Residues in contact with GLU 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLU* 2.5 26.5 - - - +
39G GLN* 3.3 19.9 + - - +
40G LYS* 3.9 26.0 + - - +
141O LYS 3.0 9.7 + - - +
142O LEU* 3.4 20.3 - - + +
144O ASN* 1.3 74.5 - - - +
146O LYS* 1.3 59.8 + - + +
148O LEU* 3.3 4.4 + - - +
149O ASN* 2.9 28.1 + - - +
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Residues in contact with LYS 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ILE 5.5 2.8 + - - -
15G PHE* 3.8 18.2 - - - -
20G GLU* 3.1 31.6 + - - -
51O GLU* 5.4 9.8 + - + +
52O GLN* 3.4 23.2 - - - +
55O VAL* 4.1 21.3 - - + +
142O LEU* 3.0 24.7 + - + +
143O THR* 3.5 7.0 - - - +
145O GLU* 1.3 75.6 - - + +
147O LEU* 1.3 60.0 + - - +
149O ASN* 3.2 10.8 + - + +
150O LEU* 2.9 23.9 + - - +
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Residues in contact with LEU 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O GLN* 3.4 32.3 - - + +
56O GLU* 4.0 6.7 - - - +
98O LEU* 5.5 0.4 - - + -
143O THR* 2.8 27.2 + - + +
144O ASN* 3.2 4.0 + - - +
146O LYS* 1.3 73.2 - - - +
148O LEU* 1.3 58.6 + - - +
150O LEU* 3.3 8.4 + - + +
151O HIS* 2.9 27.4 + - - +
166O VAL* 3.8 12.5 - - + +
170O TYR* 3.9 37.5 - - + +
171O LEU* 3.8 14.6 - - + -
174O GLN* 3.9 35.2 - - + +
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Residues in contact with LEU 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LYS* 3.6 35.0 - - + -
160G VAL* 4.1 24.8 - - + +
161G GLN* 5.2 5.4 - - + +
144O ASN* 2.9 41.0 + - - +
145O GLU* 3.7 4.5 - - - +
147O LEU* 1.3 75.0 - - - +
149O ASN* 1.3 57.2 + - - +
151O HIS* 3.4 6.3 + - + +
152O SER* 2.9 26.3 + - - -
171O LEU* 4.0 28.0 - - + -
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Residues in contact with ASN 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O ALA* 5.9 2.4 - - - +
145O GLU 2.9 14.2 + - - +
146O LYS* 3.2 15.4 + - + +
148O LEU* 1.3 75.2 - - - +
150O LEU* 1.3 64.6 + - - +
152O SER* 2.7 28.2 + - - -
153O VAL* 3.0 22.3 + - - +
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Residues in contact with LEU 150 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O ALA* 3.5 37.5 - - + +
49O VAL* 4.0 14.1 - - + +
52O GLN* 4.0 29.6 - - + +
98O LEU* 4.5 11.7 - - + -
146O LYS 2.9 13.3 + - - +
147O LEU* 3.3 11.4 + - + +
149O ASN* 1.3 77.3 - - - +
151O HIS* 1.3 63.7 + - - +
153O VAL* 3.1 7.1 + - + +
154O ALA* 3.0 20.3 + - - +
162O LEU* 4.4 11.4 - - + -
166O VAL* 3.5 30.7 - - + -
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Residues in contact with HIS 151 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G VAL* 3.3 38.8 - - + +
147O LEU 2.9 14.2 + - - +
148O LEU* 3.5 13.2 - - + +
150O LEU* 1.3 77.6 - - - +
152O SER* 1.3 57.2 + - - +
154O ALA* 3.2 7.5 + - - +
155O THR* 3.0 47.8 + - + +
163O ALA* 3.5 30.1 + - + +
166O VAL* 4.3 11.9 - - + +
167O GLU* 3.0 23.0 + - + -
171O LEU* 4.2 11.4 - - + -
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Residues in contact with SER 152 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148O LEU 2.9 14.0 + - - -
149O ASN* 2.7 31.1 + - - -
151O HIS* 1.3 74.9 + - - +
153O VAL* 1.3 61.5 + - - +
155O THR* 3.3 8.7 + - - -
156O LYS* 3.0 32.0 + - - +
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Residues in contact with VAL 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 3.9 39.0 - - + +
45O SER* 4.1 7.4 - - - +
48O ALA* 4.1 19.1 - - + -
149O ASN* 3.0 30.4 + - - +
150O LEU* 3.1 8.7 + - + +
152O SER* 1.3 78.2 - - - +
154O ALA* 1.3 63.8 + - - +
156O LYS* 3.7 9.8 - - - +
157O ASN* 3.1 45.8 + - - +
162O LEU* 5.6 0.4 - - + -
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Residues in contact with ALA 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O SER* 4.7 1.3 - - - -
150O LEU 3.0 9.8 + - - +
151O HIS* 3.4 10.8 - - - +
153O VAL* 1.3 77.9 - - - +
155O THR* 1.3 62.0 + - - +
157O ASN 3.2 2.3 + - - -
158O GLY 3.1 4.0 + - - -
159O ASP* 2.8 34.3 + - - +
162O LEU* 3.6 36.3 - - + +
163O ALA* 3.7 20.9 - - - +
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Residues in contact with THR 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O HIS* 3.0 38.7 + - + +
152O SER* 3.3 12.3 + - - -
153O VAL 3.3 0.2 - - - -
154O ALA* 1.3 71.8 - - - +
156O LYS* 1.3 69.0 + - - +
158O GLY* 3.1 14.1 + - - +
159O ASP 4.8 0.9 - - - +
163O ALA* 4.1 11.7 - - + -
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Residues in contact with LYS 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 2.8 41.1 + - - -
152O SER 3.0 16.5 + - - +
153O VAL* 3.7 10.8 - - - +
155O THR* 1.3 78.4 + - - +
157O ASN* 1.3 66.3 + - - +
158O GLY 3.5 0.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O VAL* 3.7 26.4 - - + +
44O GLU* 2.9 33.5 + - - +
45O SER* 3.7 12.2 + - - +
153O VAL* 3.1 34.3 + - - +
154O ALA 3.2 2.4 + - - +
155O THR 3.1 0.2 - - - -
156O LYS* 1.3 82.6 - - - +
158O GLY* 1.3 62.7 + - - +
159O ASP* 3.2 4.3 + - + +
----------------------------------------------------------
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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