Contacts of the helix formed by residues 25 - 59 (chain B) in PDB entry 4U0L
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 THR 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL 3.5 1.8 + - - +
24B LEU* 1.3 77.2 - - - +
26B ASP* 1.3 65.7 + - - +
27B GLU* 3.6 10.9 + - - +
28B GLU* 3.1 38.8 + - - +
29B LYS* 3.0 18.7 + - - +
122B ARG* 4.3 19.5 - - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 5.1 1.4 - - - +
25B THR* 1.3 74.5 - - - +
27B GLU* 1.3 57.6 - - - +
29B LYS* 3.7 8.1 - - - +
30B ASN* 2.8 49.4 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.6 9.4 + - - +
26B ASP* 1.3 78.3 - - - +
28B GLU* 1.3 62.8 + - + +
30B ASN* 3.8 3.4 - - - +
31B ASN* 2.8 54.1 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.5 16.2 - - + +
25B THR* 3.1 29.7 + - - +
27B GLU* 1.3 85.8 - - + +
29B LYS* 1.3 62.4 + - - +
31B ASN* 3.3 7.1 + - - +
32B LEU* 3.1 27.2 + - - +
122B ARG* 2.7 54.1 + - - +
123B PRO* 5.2 1.0 - - - +
130B MET* 3.8 29.5 - - + +
189B LYS* 4.9 4.2 + - - -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.0 19.4 - - + +
25B THR 3.0 16.9 + - - +
26B ASP* 3.9 8.7 - - - +
28B GLU* 1.3 77.1 - - - +
30B ASN* 1.3 60.9 + - - +
32B LEU* 3.3 5.8 + - - +
33B LYS* 3.1 46.0 + - + +
115B PHE* 4.1 27.8 - - + -
118B ASP* 5.6 5.6 + - - -
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Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 2.8 37.7 + - - +
27B GLU* 4.0 4.4 - - - +
29B LYS* 1.3 74.1 - - - +
31B ASN* 1.3 62.2 + - - +
33B LYS* 3.3 20.1 + - - +
34B ALA* 2.8 31.1 + - - +
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 2.8 42.0 + - - +
28B GLU* 3.5 8.3 - - - +
30B ASN* 1.3 77.0 - - - +
32B LEU* 1.3 60.4 + - + +
34B ALA* 3.3 7.1 + - - +
35B LEU* 2.9 29.3 + - - +
188B GLU* 4.5 21.0 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.6 17.5 - - + -
28B GLU 3.1 15.3 + - - +
29B LYS 3.6 6.3 - - - +
30B ASN 3.3 0.4 - - - -
31B ASN* 1.3 78.0 - - + +
33B LYS* 1.3 57.0 + - - +
35B LEU* 3.2 6.5 + - + +
36B ARG* 3.0 29.5 + - - +
115B PHE* 4.0 16.2 - - + -
120B LEU* 3.5 32.5 - - + -
130B MET* 4.6 15.3 - - + +
131B ALA 4.6 3.6 - - - +
132B ILE* 4.2 25.2 - - + +
190B THR* 3.7 34.8 - - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 3.1 36.0 + - + +
30B ASN* 3.3 18.5 + - - +
32B LEU* 1.3 75.5 - - - +
34B ALA* 1.3 62.6 + - - +
36B ARG* 3.4 29.4 + - - +
37B LYS* 3.1 22.5 + - - +
115B PHE* 3.6 24.5 - - + -
132B ILE* 5.3 0.2 - - - -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN 2.8 18.3 + - - +
31B ASN* 3.7 8.1 - - - +
33B LYS* 1.3 73.2 - - - +
35B LEU* 1.3 66.6 + - - +
37B LYS* 3.3 8.1 + - - +
38B ILE* 3.1 35.3 + - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN 2.9 17.0 + - - +
32B LEU* 3.5 10.8 - - + +
34B ALA* 1.3 77.1 - - - +
36B ARG* 1.3 62.4 + - - +
38B ILE* 3.3 8.5 + - + +
39B ILE* 3.1 41.0 + - + +
132B ILE* 5.0 1.1 - - + -
172B TRP* 3.6 36.1 - - + -
183B ILE* 5.5 1.3 - - + -
185B ILE* 4.0 15.7 - - + -
188B GLU* 5.9 0.2 - - - +
190B THR* 3.8 29.6 - - + -
192B ILE* 4.0 27.4 - - + +
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 3.0 17.1 + - - +
33B LYS* 3.7 34.0 + - - +
35B LEU* 1.3 76.4 - - - +
37B LYS* 1.3 63.1 + - - +
39B ILE* 3.2 3.1 + - - +
40B ARG* 2.9 44.0 + - - +
111B THR* 2.7 46.5 + - - +
115B PHE* 4.1 16.2 - - - -
116B GLN* 5.1 1.6 + - - -
132B ILE* 4.1 16.1 - - + +
134B ASP* 3.3 27.4 - - + +
192B ILE* 4.0 13.0 - - + +
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS 3.1 17.7 + - - +
34B ALA* 3.7 7.2 - - - +
36B ARG* 1.3 77.5 - - - +
38B ILE* 1.3 65.6 + - + +
40B ARG* 3.3 9.9 + - - +
41B LEU* 3.0 55.8 + - + +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.1 28.2 + - + +
35B LEU* 3.5 12.3 - - + +
36B ARG 3.2 0.2 - - - -
37B LYS* 1.3 79.0 - - + +
39B ILE* 1.3 66.2 + - + +
41B LEU* 3.4 9.7 + - + +
42B ARG* 3.1 22.0 + - - +
165B LEU* 3.7 29.8 - - + -
172B TRP* 4.6 18.2 - - + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.1 49.3 + - + +
36B ARG 3.2 6.7 + - - +
38B ILE* 1.3 79.1 - - + +
40B ARG* 1.3 62.5 + - + +
42B ARG* 3.2 2.3 + - - +
43B THR* 2.8 43.2 + - - +
109B PHE* 5.7 3.1 - - + -
134B ASP* 5.3 3.8 - - - +
161B SER* 3.9 0.2 + - - -
162B LEU* 3.9 17.3 - - + -
165B LEU* 3.7 23.8 - - + -
172B TRP* 4.8 0.7 - - + -
183B ILE* 4.2 7.6 - - + -
192B ILE* 4.1 21.5 - - + -
194B VAL* 4.0 24.9 - - + -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.9 42.6 + - - +
37B LYS* 3.6 9.4 - - + +
39B ILE* 1.3 77.6 - - + +
41B LEU* 1.3 58.1 + - + +
44B ARG* 3.0 29.6 + - - +
109B PHE* 3.4 55.9 + - + +
110B TRP* 4.0 7.7 - - - +
111B THR* 3.5 8.1 + - - +
134B ASP* 2.8 44.2 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 3.0 56.2 + - + +
38B ILE* 3.8 8.1 - - + +
40B ARG* 1.3 75.2 - - + +
42B ARG* 1.3 63.0 + - - +
44B ARG* 3.5 36.3 + - - +
45B ASP* 2.8 38.8 + - - +
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE 3.1 17.2 + - - +
39B ILE 3.8 0.4 - - - +
41B LEU* 1.3 76.7 - - - +
43B THR* 1.3 58.3 + - - +
45B ASP* 3.1 9.1 + - - +
46B VAL* 2.8 36.7 + - - +
75B GLN* 3.0 33.2 + - - +
161B SER* 3.5 19.7 - - - +
164B SER* 2.9 41.7 + - - +
165B LEU* 3.6 23.0 - - + +
168B GLU* 2.9 43.6 + - - -
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 2.8 26.7 + - - +
40B ARG 3.9 3.6 - - - -
42B ARG* 1.3 75.3 - - - +
44B ARG* 1.3 64.8 + - - +
46B VAL* 3.3 1.7 + - - +
47B PHE* 3.1 51.9 + - + -
107B PRO* 4.5 1.3 - - + -
109B PHE* 4.1 21.2 - - + -
136B THR* 4.3 14.0 + - + +
158B VAL* 4.5 11.4 - - + +
161B SER* 2.7 27.4 + - - -
162B LEU* 5.1 1.6 - - - +
194B VAL* 5.8 0.9 - - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 3.0 17.4 + - - +
41B LEU* 3.6 32.9 + - - +
43B THR* 1.3 78.4 - - - +
45B ASP* 1.3 88.2 + - - +
47B PHE* 3.4 2.8 + - - +
48B GLU* 3.1 32.2 + - + +
106B THR* 4.6 19.7 - - + -
107B PRO* 4.2 15.0 - - + +
109B PHE* 4.4 7.3 - - + -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 2.8 32.7 + - - +
42B ARG* 3.4 12.7 + - - +
44B ARG* 1.3 100.6 + - - +
46B VAL* 1.3 62.8 + - - +
48B GLU* 3.2 9.2 + - - +
49B GLU* 3.0 28.1 + - - +
75B GLN* 4.3 15.1 + - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 2.8 33.1 + - - +
43B THR 3.3 5.1 + - - +
45B ASP* 1.3 71.8 - - - +
47B PHE* 1.3 64.0 + - + +
49B GLU* 3.1 10.6 + - - +
50B ALA* 2.9 21.1 + - - +
75B GLN* 4.5 18.2 - - + +
76B ILE* 4.4 9.3 - - + +
157B LEU* 3.6 41.3 - - + +
160B ALA* 4.2 9.0 - - + -
161B SER* 3.7 24.7 - - - +
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.1 43.2 + - + +
44B ARG 3.7 5.2 - - - +
46B VAL* 1.3 78.1 - - + +
48B GLU* 1.3 58.3 + - + +
50B ALA* 3.3 6.0 + - - +
51B LYS* 2.8 39.6 + - + +
102B PHE* 4.5 7.2 - + - -
105B LEU* 4.2 16.2 - - + -
107B PRO* 3.8 32.8 - - + -
136B THR* 5.0 0.9 - - + -
138B MET* 3.5 39.0 - - + -
154B LEU* 4.6 11.0 - - + -
157B LEU* 3.8 37.2 - - + -
158B VAL* 4.4 8.7 - - + -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.1 25.3 + - + +
45B ASP* 3.5 10.5 - - - +
47B PHE* 1.3 73.8 - - - +
49B GLU* 1.3 56.7 + - - +
51B LYS* 2.8 37.1 + - - +
52B GLY* 2.8 32.6 + - - -
106B THR* 4.2 12.8 + - - +
107B PRO* 5.8 0.5 - - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.0 17.2 + - + +
46B VAL* 3.1 11.5 + - - +
48B GLU* 1.3 76.6 - - + +
50B ALA* 1.3 62.0 + - - +
52B GLY* 3.3 9.3 + - - -
53B ILE* 3.3 20.9 + - - +
74B THR* 3.3 22.8 - - + +
75B GLN* 2.9 59.8 + - - +
76B ILE* 4.5 3.4 + - + +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL 2.9 12.1 + - - +
47B PHE 3.5 8.3 - - - +
49B GLU* 1.3 77.7 - - - +
51B LYS* 1.3 62.1 + - - +
53B ILE* 3.1 11.8 + - - +
54B ALA* 3.0 17.5 + - - +
76B ILE* 4.6 9.8 - - + +
91B ILE* 4.5 10.5 - - + +
102B PHE* 3.6 22.7 - - + -
153B LEU* 6.1 0.4 - - + -
157B LEU* 3.8 26.5 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 2.8 32.0 + - + +
48B GLU* 2.8 37.0 + - - +
50B ALA* 1.3 73.3 - - - +
52B GLY* 1.3 55.8 + - - +
54B ALA* 3.2 2.3 + - - +
55B LYS* 2.9 31.2 + - - +
102B PHE* 3.6 34.8 - - + +
103B LEU* 3.7 36.7 + - + +
104B GLY 4.8 1.0 + - - -
105B LEU* 2.6 31.3 + - + +
106B THR* 3.7 8.7 + - - +
107B PRO* 6.0 0.2 - - + -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU 2.8 20.3 + - - -
49B GLU* 3.7 3.8 - - - -
50B ALA 3.2 0.8 - - - -
51B LYS* 1.3 73.3 - - - +
53B ILE* 1.3 61.0 + - - +
55B LYS* 3.7 7.8 + - - +
56B ALA* 3.3 19.9 + - - +
70B LYS* 5.5 0.2 + - - -
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU 3.4 12.3 - - - +
50B ALA* 3.1 9.1 + - - +
52B GLY* 1.3 74.5 - - - +
54B ALA* 1.3 60.0 + - - +
55B LYS 3.1 1.8 - - - -
56B ALA* 2.9 23.3 + - + +
57B VAL* 3.3 10.8 + - + +
62B LEU* 6.1 0.7 - - + -
67B ILE* 4.3 20.0 - - + -
70B LYS* 3.9 26.7 - - + +
71B VAL* 3.8 38.4 - - + +
74B THR* 4.0 14.8 - - + -
76B ILE* 5.1 2.7 - - + -
91B ILE* 4.2 24.7 - - + -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA 3.0 5.8 + - - +
51B LYS* 3.2 3.3 + - - +
53B ILE* 1.3 76.2 - - - +
55B LYS* 1.3 61.5 + - - +
57B VAL* 3.3 13.0 + - - +
58B LYS* 3.3 11.3 + - - +
91B ILE* 4.4 12.5 - - + +
94B MET* 4.2 15.3 - - + -
99B ARG* 3.7 15.3 - - + +
102B PHE* 3.6 37.2 - - + -
103B LEU* 4.6 5.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS 2.9 16.8 + - - +
52B GLY* 3.8 9.2 - - - +
53B ILE 3.1 0.2 - - - -
54B ALA* 1.3 75.6 - - - +
56B ALA* 1.3 58.2 + - - +
57B VAL 3.1 6.2 + - - -
58B LYS* 3.7 3.8 + - + +
59B LYS* 3.2 37.3 + - + +
103B LEU* 3.6 30.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY 3.3 11.0 + - - +
53B ILE 2.9 13.1 + - - +
55B LYS* 1.3 77.6 - - - +
57B VAL* 1.3 56.7 + - - +
59B LYS* 4.5 11.9 - - - +
60B SER* 3.7 5.5 + - - +
62B LEU* 3.1 27.1 - - + +
70B LYS* 3.6 26.2 - - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE 3.3 13.4 + - - +
54B ALA* 3.7 7.6 - - - +
55B LYS 3.1 0.8 - - - -
56B ALA* 1.3 82.3 - - - +
58B LYS* 1.3 66.2 + - - +
59B LYS 3.0 2.0 + - - -
60B SER 3.2 21.2 + - - -
61B ALA* 3.5 5.7 + - - -
62B LEU* 4.7 12.6 - - + +
67B ILE* 3.9 33.7 - - + -
91B ILE* 4.4 13.9 - - + +
92B TYR* 5.4 1.3 - - + +
99B ARG* 3.4 35.0 + - - +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 3.3 7.6 + - - +
55B LYS* 4.3 4.9 - - + +
57B VAL* 1.3 78.7 - - - +
59B LYS* 1.3 59.0 + - - +
96B ASP* 6.1 3.4 - - + -
99B ARG* 3.7 31.1 - - + +
100B ASP* 2.7 45.8 + - - +
103B LEU* 5.0 16.1 - - + +
----------------------------------------------------------
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 3.2 31.9 + - + +
56B ALA* 4.5 7.8 - - - +
57B VAL 3.0 0.8 - - - -
58B LYS* 1.3 80.7 - - - +
60B SER* 1.3 69.8 + - - +
----------------------------------------------------------
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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