Contacts of the helix formed by residues 127 - 157 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N ASP* 5.1 0.4 - - - -
123N HIS* 2.9 22.0 + - - -
124N ALA 4.9 0.4 - - - -
125N ASP 3.3 2.2 + - - -
126N LYS* 1.3 79.2 - - - +
128N ASP* 1.3 67.9 + - - -
129N ALA 3.3 2.6 + - - -
130N LEU 3.5 0.8 + - - -
131N HIS* 3.1 22.2 + - - +
193N LYS* 4.0 17.0 - - - +
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Residues in contact with ASP 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N TYR* 4.2 10.4 + - + +
70N PHE* 3.6 15.8 - - + -
75N VAL* 3.7 15.8 - - - +
77N LEU* 4.0 1.2 - - - +
121N PHE 3.6 20.2 - - - +
122N ASP* 3.9 17.4 + - - +
123N HIS 4.4 0.7 - - - +
127N GLY* 1.3 73.8 - - - +
129N ALA* 1.3 71.5 + - - +
131N HIS* 3.4 1.4 + - - +
132N ALA* 3.0 26.5 + - - +
197N VAL* 5.0 0.5 - - - +
190S ARG* 3.1 40.1 + - - -
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Residues in contact with ALA 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N PHE* 4.3 0.7 - - - -
77N LEU* 4.1 5.6 - - + -
80N LEU* 3.7 28.1 - - + +
127N GLY 3.4 1.0 - - - -
128N ASP* 1.3 82.9 + - - +
130N LEU* 1.3 63.1 + - - +
132N ALA* 3.3 1.7 + - - +
133N MET* 3.0 28.1 + - - +
188N LEU* 3.9 15.9 - - + -
197N VAL* 3.7 32.5 - - + -
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Residues in contact with LEU 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N LYS* 3.6 37.9 - - + +
127N GLY 3.5 1.6 + - - -
128N ASP 3.4 0.2 - - - -
129N ALA* 1.3 78.2 - - - +
131N HIS* 1.3 65.4 + - - +
133N MET 3.3 1.0 + - - -
134N GLU* 2.9 51.6 + - - +
185N VAL* 3.8 28.5 - - + +
188N LEU* 4.0 20.5 - - + +
189N ARG* 3.9 26.9 - - + +
197N VAL* 5.8 2.6 - - + +
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Residues in contact with HIS 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N LEU* 6.0 3.6 - - + -
120N ASP 5.4 1.3 - - - -
121N PHE* 3.4 25.9 + + - +
122N ASP 3.9 11.7 + - - -
123N HIS* 3.6 35.1 + + + -
126N LYS* 4.2 14.5 - - + +
127N GLY 3.1 19.4 + - - +
128N ASP 3.7 2.9 - - - +
130N LEU* 1.3 77.4 - - - +
132N ALA* 1.3 55.9 + - - +
134N GLU* 3.3 3.8 + - - +
135N LEU* 2.9 59.6 + - + +
25Q LEU* 4.4 14.8 - - + +
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Residues in contact with ALA 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N MET* 3.9 8.7 - - - +
70N PHE* 3.4 41.1 - - + -
80N LEU* 4.7 0.4 - - + -
84N PHE* 4.1 13.2 - - + -
121N PHE* 4.6 7.2 - - + -
128N ASP 3.0 7.1 + - - +
129N ALA 3.8 2.5 - - - +
130N LEU 3.3 0.2 - - - -
131N HIS* 1.3 77.7 + - - +
133N MET* 1.3 58.7 + - - +
135N LEU* 3.2 12.4 + - - +
136N ALA* 2.8 28.9 + - - +
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Residues in contact with MET 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N LEU* 4.3 10.5 - - + -
83N PHE* 3.6 30.5 - - + -
84N PHE* 4.2 12.3 - - + -
129N ALA 3.0 14.2 + - - +
130N LEU 3.8 2.5 - - - +
132N ALA* 1.3 77.3 - - - +
134N GLU* 1.3 57.6 + - - +
136N ALA* 3.3 1.5 + - - -
137N LEU* 2.8 25.3 + - - +
181N ILE* 3.5 19.0 - - - +
184N TYR* 3.6 39.0 - - + -
185N VAL* 3.8 17.7 - - + +
188N LEU* 3.6 24.7 - - + -
200N PHE* 4.7 2.0 - - + -
204N LEU* 4.0 16.6 - - + -
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Residues in contact with GLU 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N LYS* 3.3 35.4 + - - +
130N LEU* 2.9 38.8 + - + +
131N HIS* 3.7 4.9 - - + +
133N MET* 1.3 76.2 - - - +
135N LEU* 1.3 58.0 + - - +
137N LEU* 3.4 5.1 + - - +
138N SER* 3.0 31.0 + - - -
185N VAL* 4.0 14.8 - - + -
189N ARG* 2.7 35.3 + - - +
25Q LEU* 3.7 17.7 - - + +
28Q VAL* 4.5 14.7 - - + +
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Residues in contact with LEU 135 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N MET* 3.8 8.5 - - + -
118N LEU* 5.2 4.3 - - + -
121N PHE* 3.7 29.6 - - + -
131N HIS* 2.9 44.5 + - + +
132N ALA* 3.5 8.3 - - - +
134N GLU* 1.3 74.7 - - - +
136N ALA* 1.3 60.3 + - - +
138N SER* 3.2 3.3 + - - -
139N LEU* 2.9 38.2 + - + +
18Q PHE* 4.8 12.6 - - + -
21Q VAL* 4.7 15.9 - - + -
25Q LEU* 3.5 33.7 - - + -
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Residues in contact with ALA 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N TYR* 3.9 28.7 - - + +
66N MET* 4.1 3.5 - - - +
83N PHE* 5.3 0.2 - - + -
84N PHE* 4.1 13.5 - - + -
132N ALA 2.8 16.9 + - - +
133N MET* 3.3 8.7 + - - +
135N LEU* 1.3 76.3 - - - +
137N LEU* 1.3 62.7 + - - +
139N LEU* 3.2 7.1 + - - +
140N GLU* 3.0 28.7 + - - +
181N ILE* 4.3 13.0 - - + -
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Residues in contact with LEU 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133N MET 2.8 16.6 + - - +
134N GLU* 3.6 6.1 - - - +
135N LEU 3.3 0.2 - - - -
136N ALA* 1.3 75.2 - - - +
138N SER* 1.3 57.9 + - - +
140N GLU* 3.2 3.8 + - + -
141N LYS* 2.9 41.1 + - + +
178N ILE* 3.8 28.3 - - + +
181N ILE* 3.7 12.5 - - + +
182N SER* 3.4 31.2 - - - +
185N VAL* 4.5 8.3 - - + -
28Q VAL* 4.4 21.8 - - + -
36Q LEU* 3.8 27.8 - - + +
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Residues in contact with SER 138 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134N GLU 3.0 15.4 + - - -
135N LEU* 3.2 9.2 + - - -
137N LEU* 1.3 76.6 - - - +
139N LEU* 1.3 57.7 + - - +
141N LYS* 3.4 3.0 + - - -
142N LEU* 2.9 29.3 + - - +
21Q VAL* 3.5 20.3 - - - +
24Q GLU* 3.4 19.2 + - - +
25Q LEU* 3.1 34.5 - - - +
28Q VAL* 3.6 5.9 - - - +
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Residues in contact with LEU 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N VAL* 4.3 26.7 - - + -
62N VAL* 4.6 24.7 - - + -
63N TYR* 4.8 7.4 - - + +
66N MET* 5.0 2.0 - - + -
135N LEU* 2.9 33.2 + - + +
136N ALA* 3.5 11.2 - - - +
138N SER* 1.3 77.0 - - - +
140N GLU* 1.3 57.9 + - - +
142N LEU* 3.3 13.2 + - + +
143N THR* 2.9 32.3 + - - -
15Q PHE* 5.5 0.7 - - + -
17Q PRO* 4.2 23.6 - - + -
18Q PHE* 5.1 6.7 - - + -
21Q VAL* 3.7 26.9 - - + -
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Residues in contact with GLU 140 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N VAL* 4.4 3.6 - - - +
63N TYR* 2.5 34.7 + - - +
91N GLU* 3.6 15.7 - - - +
136N ALA 3.0 20.1 + - - +
137N LEU* 3.2 4.5 + - - +
139N LEU* 1.3 74.0 - - - +
141N LYS* 1.3 61.8 + - - +
143N THR* 3.3 5.9 + - - +
144N ASN* 2.9 24.4 + - - +
174N GLN* 2.7 47.0 + - - +
177N ALA* 4.1 12.3 - - + +
178N ILE* 3.9 12.8 - - + -
181N ILE* 3.5 20.0 - - + +
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Residues in contact with LYS 141 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N LEU* 2.9 36.1 + - + +
138N SER* 3.7 5.4 - - - +
140N GLU* 1.3 74.8 - - - +
142N LEU* 1.3 64.4 + - - +
144N ASN* 3.3 0.7 + - - +
145N GLU* 3.0 12.6 + - - +
178N ILE* 4.1 8.7 - - + -
24Q GLU* 3.9 25.3 + - + +
27Q LEU* 5.7 2.8 + - - +
28Q VAL* 5.7 4.6 - - + +
29Q PRO* 5.0 9.5 - - - +
35Q SER 5.5 0.2 + - - -
36Q LEU 2.7 29.9 + - - -
37Q ALA 3.7 14.1 - - - -
38Q ARG 3.4 18.7 + - - -
39Q GLN* 2.9 47.6 + - + +
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Residues in contact with LEU 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N VAL* 6.3 0.4 - - + -
138N SER 2.9 17.7 + - - +
139N LEU* 3.5 11.7 - - + +
141N LYS* 1.3 77.2 - - - +
143N THR* 1.3 62.1 + - - +
145N GLU* 3.3 20.5 + - - +
146N LYS* 3.0 32.7 + - + +
15Q PHE* 3.3 35.0 - - + -
17Q PRO* 4.3 12.3 - - + +
20Q GLU* 3.6 45.8 - - + +
21Q VAL* 4.5 10.8 - - + +
24Q GLU* 4.6 7.8 - - + +
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Residues in contact with THR 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N GLN* 4.0 5.8 - - - +
55N VAL* 4.3 6.7 - - + +
56N GLU* 3.5 26.9 - - - +
59N VAL* 3.5 24.7 - - + +
91N GLU* 5.3 0.2 + - - -
139N LEU 2.9 14.5 + - - -
140N GLU* 3.6 12.2 + - - -
142N LEU* 1.3 76.8 - - - +
144N ASN* 1.3 57.9 + - - +
146N LYS* 3.2 7.9 + - - +
147N LEU* 2.9 30.4 + - + +
174N GLN* 3.5 19.5 - - - +
214N CA 4.1 8.1 - - - -
15Q PHE* 6.1 0.2 - - - -
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Residues in contact with ASN 144 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N GLU 2.9 13.8 + - - +
141N LYS 3.5 3.1 - - - +
142N LEU 3.2 0.2 - - - -
143N THR* 1.3 76.5 - - - +
145N GLU* 1.3 63.4 + - - +
147N LEU* 3.2 3.8 + - - +
148N LEU* 2.9 42.2 + - - +
171N LEU* 4.2 15.4 - - - +
174N GLN* 3.4 29.9 - - + +
175N VAL* 5.2 9.9 - - - +
178N ILE* 3.9 7.9 - - + +
39Q GLN* 2.9 37.4 + - - +
105Q ARG* 6.1 0.4 - - - +
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Residues in contact with GLU 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N LYS 3.0 12.2 + - - +
142N LEU* 3.5 24.7 - - + +
144N ASN* 1.3 75.8 - - - +
146N LYS* 1.3 59.9 + - + +
148N LEU* 3.3 7.4 + - - +
149N ASN* 2.9 48.3 + - - +
20Q GLU* 5.9 2.0 - - - -
24Q GLU* 4.3 12.1 - - - +
39Q GLN* 4.0 10.6 + - - +
40Q LYS* 4.3 25.8 + - - +
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Residues in contact with LYS 146 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N GLU* 5.6 7.0 + - + +
52N GLN* 3.4 23.2 - - - +
55N VAL* 4.1 20.8 - - + +
142N LEU* 3.0 25.9 + - + +
143N THR* 3.2 7.4 + - - +
145N GLU* 1.3 79.2 - - + +
147N LEU* 1.3 58.3 + - - +
149N ASN* 3.2 19.5 + - + +
150N LEU* 2.9 24.1 + - - +
14Q ILE 5.7 2.0 + - - -
15Q PHE* 3.9 18.1 - - + +
20Q GLU* 2.9 39.6 + - - -
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Residues in contact with LEU 147 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N GLN* 3.5 31.2 - - + +
56N GLU* 4.0 6.7 - - - +
98N LEU* 5.5 0.4 - - + -
143N THR* 2.9 20.3 + - + +
144N ASN* 3.2 6.5 + - - +
146N LYS* 1.3 73.6 - - - +
148N LEU* 1.3 60.6 + - - +
150N LEU* 3.2 9.2 + - + +
151N HIS* 2.9 27.4 + - - +
166N VAL* 3.8 12.6 - - + +
170N TYR* 3.8 38.1 - - + +
171N LEU* 3.8 15.7 - - + -
174N GLN* 3.8 37.2 - - + +
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Residues in contact with LEU 148 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N ASN* 2.9 41.0 + - - +
145N GLU* 3.7 4.9 - - - +
147N LEU* 1.3 75.2 - - - +
149N ASN* 1.3 59.2 - - - +
151N HIS* 3.3 6.7 + - + +
152N SER* 2.9 30.4 + - - -
171N LEU* 4.0 27.8 - - + -
40Q LYS* 3.7 35.7 - - + -
158Q GLY 5.4 2.7 - - - +
160Q VAL* 4.3 22.1 - - + +
161Q GLN* 5.3 4.0 - - + +
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Residues in contact with ASN 149 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145N GLU* 2.9 37.2 + - - +
146N LYS* 3.4 22.1 - - + +
148N LEU* 1.3 76.7 - - - +
150N LEU* 1.3 60.1 + - - +
152N SER* 3.0 10.4 + - - -
153N VAL* 2.8 35.4 + - + +
40Q LYS* 6.0 1.0 - - - -
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Residues in contact with LEU 150 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ALA* 3.5 40.4 - - + +
49N VAL* 4.0 13.9 - - + +
52N GLN* 4.0 29.8 - - + +
98N LEU* 4.5 12.6 - - + -
146N LYS 2.9 13.7 + - - +
147N LEU* 3.2 11.2 + - + +
149N ASN* 1.3 75.7 - - - +
151N HIS* 1.3 62.5 + - - +
153N VAL* 3.2 5.7 + - - +
154N ALA* 3.0 21.0 + - - +
162N LEU* 4.5 9.0 - - + -
166N VAL* 3.6 28.9 - - + -
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Residues in contact with HIS 151 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N LEU 2.9 12.7 + - - +
148N LEU* 3.4 12.6 - - - +
150N LEU* 1.3 75.3 - - - +
152N SER* 1.3 59.4 + - - +
154N ALA* 3.3 7.9 + - - +
155N THR* 2.9 54.7 + - + +
163N ALA* 3.3 29.3 + - + +
166N VAL* 4.3 10.9 - - + +
167N GLU* 2.9 31.1 + - + -
171N LEU* 4.3 5.4 - - + -
160Q VAL* 3.3 39.4 - - + +
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Residues in contact with SER 152 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N LEU 2.9 17.3 + - - -
149N ASN* 3.0 14.9 + - - -
151N HIS* 1.3 74.1 + - - +
153N VAL* 1.3 60.4 + - - +
155N THR* 2.7 21.8 + - - -
156N LYS* 2.8 19.2 + - - +
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Residues in contact with VAL 153 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLU* 3.6 30.3 - - + +
45N SER* 4.4 4.3 - - - -
48N ALA* 4.0 26.5 - - + -
149N ASN* 2.8 22.7 + - + +
150N LEU 3.2 6.9 + - - +
152N SER* 1.3 75.7 - - - +
154N ALA* 1.3 63.7 + - - +
156N LYS* 3.3 9.8 + - - +
157N ASN* 3.0 46.3 + - - +
162N LEU* 5.9 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N SER* 4.7 2.2 - - - -
150N LEU 3.0 10.9 + - - +
151N HIS* 3.4 10.3 - - - +
153N VAL* 1.3 77.6 - - - +
155N THR* 1.3 56.5 + - - +
157N ASN 3.3 1.7 + - - -
158N GLY 3.0 7.4 + - - -
159N ASP* 2.8 36.7 + - - +
162N LEU* 3.7 35.8 - - + +
163N ALA* 3.7 19.3 - - - +
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Residues in contact with THR 155 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151N HIS* 2.9 42.4 + - + +
152N SER* 2.7 25.1 + - - -
154N ALA* 1.3 74.2 - - - +
156N LYS* 1.3 64.7 + - - +
158N GLY* 3.0 14.0 + - - +
159N ASP 5.4 0.4 - - - -
163N ALA* 4.3 8.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLU* 2.7 39.6 + - - +
152N SER 2.8 20.5 + - - +
153N VAL* 3.7 10.9 - - - +
155N THR* 1.3 75.1 + - - +
157N ASN* 1.3 62.2 + - - +
158N GLY 3.5 0.5 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N VAL* 3.8 27.9 - - + +
44N GLU* 2.8 41.2 + - - +
45N SER* 4.1 13.2 + - - +
153N VAL* 3.0 30.5 + - - +
154N ALA 4.0 2.5 - - - +
156N LYS* 1.3 81.9 - - - +
158N GLY* 1.3 63.5 + - - +
159N ASP* 3.2 3.9 + - + +
----------------------------------------------------------
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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