Contacts of the helix formed by residues 23 - 60 (chain B) in PDB entry 2RAX
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 SER 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 4.6 18.2 + - - +
20B LYS 2.9 12.1 + - - -
21B LEU* 4.6 5.0 - - - +
22B ALA* 1.3 76.4 - - - +
24B PHE* 1.3 56.9 + - - +
25B LEU 3.1 2.2 - - - +
26B LYS* 3.1 16.7 + - - +
27B ASP* 2.9 37.6 + - - +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.3 35.5 - - + +
22B ALA* 4.2 0.2 - - - -
23B SER* 1.3 79.2 + - - +
25B LEU* 1.3 71.8 + - + +
27B ASP* 3.4 12.8 + - + +
28B PHE* 3.1 20.4 + - - +
53F LEU* 3.4 42.6 - - + -
57F GLU* 3.8 26.7 - - + -
60F ARG* 5.6 6.1 - - - -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 4.7 0.7 - - - +
22B ALA* 3.8 25.4 - - + +
23B SER 3.1 1.0 - - - -
24B PHE* 1.3 92.8 - - + +
26B LYS* 1.3 57.3 + - - +
27B ASP 2.9 1.3 - - - -
28B PHE* 2.9 9.0 + - + +
29B ASP* 2.7 37.2 + - - +
10E TRP* 3.5 33.9 - - + -
102E LEU* 4.2 13.5 - - + -
105E ASP* 3.8 0.7 - - - +
53F LEU* 6.4 0.9 - - + -
54F TYR* 3.5 42.4 - - + +
57F GLU* 5.1 9.0 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 4.8 1.0 + - - +
23B SER* 3.1 23.1 + - - +
25B LEU* 1.3 75.2 - - - +
27B ASP* 1.3 64.0 + - - +
29B ASP* 3.8 8.8 + - - +
30B ARG* 3.3 21.7 + - - +
7E PRO* 5.4 13.2 - - + -
8E PRO* 6.1 2.2 - - + -
10E TRP* 5.7 1.0 - - - -
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 2.9 17.5 + - - +
24B PHE* 3.4 16.4 - - + +
25B LEU 2.9 0.6 - - - -
26B LYS* 1.3 78.2 - - - +
28B PHE* 1.3 65.5 + - - +
30B ARG* 3.1 9.5 + - - +
31B GLU* 3.0 19.1 + - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE 3.1 10.6 + - - +
25B LEU* 2.9 11.7 + - + +
27B ASP* 1.3 74.0 - - - +
29B ASP* 1.3 60.1 + - - +
31B GLU* 2.9 33.0 + - + +
32B VAL* 2.7 54.2 + - + +
35B ARG* 5.1 7.0 - - - -
109E ALA* 5.6 1.8 - - + -
46F LEU* 5.2 1.3 - - + -
49F GLU* 4.2 9.0 - - + -
50F VAL* 3.5 44.6 - - + -
53F LEU* 3.3 37.0 - - + -
54F TYR* 4.3 20.2 - + - -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU 2.7 19.7 + - - +
26B LYS* 3.8 9.4 - - - +
28B PHE* 1.3 73.1 - - - +
30B ARG* 1.3 56.1 + - - +
32B VAL* 3.6 8.7 + - - +
33B GLU* 2.8 40.9 + - - +
9E ALA* 4.4 20.3 - - + +
108E ARG* 5.3 4.3 + - - -
112E LYS* 3.3 24.4 + - - +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS 3.3 10.8 + - - +
27B ASP* 3.1 12.7 + - - +
28B PHE 3.0 0.4 - - - -
29B ASP* 1.3 79.5 + - - +
31B GLU* 1.3 55.3 + - - +
33B GLU* 3.1 34.2 + - - +
34B ILE* 2.8 73.3 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP 3.0 11.0 + - - +
28B PHE* 2.9 30.2 + - + +
30B ARG* 1.3 72.4 - - - +
32B VAL* 1.3 68.7 + - - +
34B ILE* 2.9 17.3 + - + +
35B ARG* 2.8 55.1 + - - +
49F GLU* 4.6 1.7 - - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 2.7 57.9 + - + +
29B ASP* 3.7 8.1 - - - +
31B GLU* 1.3 73.5 - - - +
33B GLU* 1.3 58.4 + - - +
35B ARG* 3.6 7.4 - - - +
36B ILE* 2.9 41.6 + - + +
109E ALA* 5.2 9.4 - - + +
112E LYS* 5.0 11.9 - - + +
113E ILE* 3.6 25.1 - - + -
46F LEU* 4.4 8.5 - - + -
50F VAL* 4.1 9.6 - - + -
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 2.8 33.6 + - - +
30B ARG* 3.2 35.8 + - - +
31B GLU 2.9 0.4 + - - -
32B VAL* 1.3 71.3 - - - +
34B ILE* 1.3 65.9 + - - +
36B ILE* 3.4 9.0 + - - +
37B LYS* 3.2 20.3 + - - +
112E LYS* 4.2 18.8 + - - +
116E GLU* 5.3 5.8 - - - +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG* 2.8 54.0 + - + +
31B GLU* 3.2 14.8 - - + +
33B GLU* 1.3 77.1 - - - +
35B ARG* 1.3 65.7 + - + +
37B LYS* 3.2 10.3 + - - +
38B GLN* 3.1 28.4 + - + +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 5.1 2.8 - - - -
31B GLU* 2.8 46.9 + - - +
32B VAL 3.6 5.2 - - - +
34B ILE* 1.3 77.3 - - + +
36B ILE* 1.3 68.2 + - - +
38B GLN* 3.2 9.1 + - + +
39B ILE* 3.1 26.8 + - + +
42F ASP 5.6 1.2 + - - -
45F ASN* 4.8 2.8 - - - +
46F LEU* 3.5 45.5 - - + +
49F GLU* 2.7 44.8 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 2.9 32.2 + - + +
33B GLU* 3.6 9.4 - - - +
34B ILE 3.3 0.2 - - - -
35B ARG* 1.3 74.1 - - - +
37B LYS* 1.3 67.4 + - - +
39B ILE* 2.8 17.8 + - + +
40B GLU* 2.9 16.7 + - + -
112E LYS* 5.1 4.9 - - + +
113E ILE* 3.6 46.9 - - + +
116E GLU* 3.4 46.0 - - + +
117E THR* 4.3 11.2 - - - +
46F LEU* 3.7 10.5 - - + -
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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
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33B GLU 3.2 8.0 + - - +
34B ILE* 3.2 12.1 + - - +
36B ILE* 1.3 79.9 - - - +
38B GLN* 1.3 67.7 + - - +
40B GLU* 3.2 6.5 + - - +
41B SER* 3.0 25.7 + - - -
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 3.1 19.0 + - + +
35B ARG* 3.5 14.4 - - + +
36B ILE 3.1 0.6 - - - -
37B LYS* 1.3 80.5 - - - +
39B ILE* 1.3 61.8 + - + +
41B SER* 3.7 11.4 + - - -
42B ASP* 3.2 31.4 + - - +
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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
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35B ARG* 3.1 17.1 + - + +
36B ILE* 2.8 8.2 + - - +
38B GLN* 1.3 72.8 - - + +
40B GLU* 1.3 59.6 + - - +
41B SER 3.0 1.6 - - - -
42B ASP* 2.7 31.3 + - + +
43B ARG* 2.9 12.4 + - + -
113E ILE* 5.7 0.2 - - + -
117E THR* 3.9 31.2 - - + +
39F ILE* 3.9 22.9 - - + -
42F ASP* 4.0 18.8 - - + +
43F ARG* 3.8 33.2 - - + +
46F LEU* 4.2 15.5 - - + -
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 2.9 19.3 + - + +
37B LYS* 3.7 10.8 - - - +
39B ILE* 1.3 75.3 - - - +
41B SER* 1.3 51.5 + - - +
43B ARG* 3.5 27.1 + - - +
44B GLN* 2.7 63.8 + - - +
116E GLU* 3.0 31.7 - - + +
117E THR* 4.0 7.1 + - - +
119E ASN* 4.3 10.1 - - - +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS 3.0 16.7 + - - -
38B GLN* 3.7 15.5 + - - -
39B ILE 2.8 0.6 + - - -
40B GLU* 1.3 74.5 - - - +
42B ASP* 1.3 63.0 + - - +
44B GLN* 4.1 6.5 - - - -
45B ASN* 2.6 51.5 + - - -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 3.2 18.7 + - - +
39B ILE* 2.7 16.9 + - - +
41B SER* 1.3 82.2 + - - +
43B ARG* 1.3 60.1 + - - +
45B ASN* 3.6 8.1 + - - +
46B LEU* 3.1 22.2 + - - +
35F ARG* 5.4 1.0 + - - -
38F GLN* 6.0 1.6 - - - +
39F ILE* 4.1 23.7 - - + +
42F ASP* 4.7 9.9 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.0 13.5 + - + +
114A ALA* 3.9 31.1 + - - +
117A THR* 3.7 32.8 + - - +
39B ILE* 2.9 11.2 + - + +
40B GLU* 3.5 20.7 + - - +
42B ASP* 1.3 75.8 - - - +
44B GLN* 1.3 63.9 + - - +
46B LEU* 3.4 3.8 + - - +
47B LEU* 3.2 44.4 + - + +
117E THR* 3.3 21.2 + - - +
118E ASN 3.0 27.7 + - - -
119E ASN 3.2 14.6 + - - -
39F ILE* 3.9 22.3 - - + +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 2.7 54.9 + - - +
41B SER* 3.0 7.6 + - - +
43B ARG* 1.3 72.7 - - - +
45B ASN* 1.3 66.4 - - - +
47B LEU* 3.5 25.6 + - - +
48B LYS* 3.2 20.3 + - - +
119E ASN 4.6 10.9 + - - -
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 2.6 37.6 + - - +
42B ASP* 3.6 8.2 + - - +
44B GLN* 1.3 70.9 - - - +
46B LEU* 1.3 66.0 + - - +
48B LYS* 2.7 24.9 + - - +
49B GLU* 2.9 27.0 + - + +
35F ARG* 5.1 2.9 - - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.2 28.9 - - + -
42B ASP 3.1 13.1 + - - +
43B ARG 3.6 6.1 - - - +
44B GLN 3.4 0.2 - - - -
45B ASN* 1.3 77.2 - - - +
47B LEU* 1.3 63.9 + - - +
49B GLU* 3.0 16.6 + - + +
50B VAL* 3.1 13.5 + - + +
28F PHE* 5.3 1.6 - - + -
32F VAL* 4.3 21.1 - - + -
35F ARG* 3.6 57.4 - - + +
36F ILE* 4.3 9.0 - - + +
39F ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 3.9 29.3 - - + +
113A ILE* 3.8 33.4 - - + -
114A ALA* 5.2 2.5 - - + +
43B ARG* 3.3 34.3 - - + +
44B GLN* 3.7 33.9 - - - +
45B ASN 3.2 0.6 - - - -
46B LEU* 1.3 75.9 - - - +
48B LYS* 1.3 61.9 + - - +
50B VAL* 3.2 11.4 + - - +
51B ASP* 3.1 27.0 + - - +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN 3.2 10.3 + - - +
45B ASN* 2.7 24.4 + - - +
47B LEU* 1.3 75.1 - - - +
49B GLU* 1.3 54.8 + - + +
51B ASP* 3.3 10.3 + - + +
52B ASN* 2.9 41.3 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN* 2.9 23.2 + - + +
46B LEU* 3.0 7.4 + - + +
48B LYS* 1.3 76.2 - - + +
50B VAL* 1.3 59.4 - - - +
52B ASN* 3.3 11.8 - - - +
53B LEU* 2.9 31.9 + - - +
28F PHE* 4.4 10.3 - - + -
31F GLU* 4.5 1.9 - - - +
35F ARG* 3.0 41.4 + - - +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 3.7 25.1 - - + +
109A ALA* 4.0 11.4 - - + -
110A LYS* 3.8 15.0 - - + -
113A ILE* 4.6 13.0 - - + -
46B LEU* 3.1 15.5 + - + +
47B LEU* 3.4 9.6 - - - +
49B GLU* 1.3 74.4 - - - +
51B ASP* 1.3 69.5 + - - +
53B LEU* 3.8 0.2 - - - +
54B TYR* 3.2 35.4 + - + +
28F PHE* 3.8 26.7 - - + -
32F VAL* 4.5 10.1 - - + -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.6 22.9 + - - -
110A LYS* 3.2 38.9 + - - +
47B LEU* 3.1 11.0 + - - +
48B LYS* 3.4 13.3 - - + +
50B VAL* 1.3 82.0 - - - +
52B ASN* 1.3 65.7 + - - +
54B TYR* 4.1 0.7 - - - +
55B ASN* 2.9 31.3 + - - +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LYS* 2.9 34.9 + - - +
49B GLU* 3.3 15.0 - - - +
51B ASP* 1.3 75.3 - - - +
53B LEU* 1.3 65.2 + - - +
55B ASN* 3.1 4.8 + - - +
56B ILE* 2.9 30.3 + - + +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU 2.9 17.0 + - - +
50B VAL* 3.8 3.8 - - - +
52B ASN* 1.3 75.8 - - - +
54B TYR* 1.3 69.7 + - + +
56B ILE* 2.9 21.5 + - + +
57B GLU* 3.0 19.1 + - + +
24F PHE* 3.5 39.3 - - + -
25F LEU* 5.2 5.6 - - + -
28F PHE* 3.3 51.8 - - + -
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.3 30.1 - - + -
105A ASP* 2.4 30.2 + - + -
106A ARG* 3.4 45.1 - - + -
109A ALA* 4.4 9.8 - - + +
50B VAL* 3.2 33.8 + - + +
53B LEU* 1.3 82.9 - - + +
55B ASN* 1.3 52.8 + - - +
57B GLU* 3.0 8.9 + - + +
58B ILE* 2.7 42.8 + - + +
25F LEU* 3.6 35.2 - - + +
28F PHE* 4.5 16.3 - + - -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.1 38.3 + - - +
51B ASP* 2.9 29.4 + - - +
52B ASN* 3.5 4.7 - - - +
54B TYR* 1.3 72.8 - - - +
56B ILE* 1.3 65.4 + - - +
58B ILE* 3.4 17.0 - - - +
59B LEU* 3.1 29.7 + - + +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 2.9 23.3 + - + +
53B LEU* 2.9 13.6 + - + +
55B ASN* 1.3 75.6 - - - +
57B GLU* 1.3 75.4 + - - +
59B LEU* 3.0 8.0 + - + +
60B ARG* 2.8 55.1 + - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 5.0 15.0 - - + -
53B LEU* 3.0 18.8 + - + +
54B TYR* 3.5 9.2 - - - +
56B ILE* 1.3 86.6 - - - +
58B ILE* 1.3 61.7 + - - +
60B ARG* 2.8 53.9 + - - +
61B LEU* 3.3 18.7 - - + +
21F LEU* 5.8 3.8 - - - +
24F PHE* 3.4 35.7 - - + -
25F LEU* 4.4 11.2 - - + -
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 5.0 11.4 - - - -
102A LEU* 3.7 22.2 - - + +
103A LYS* 3.9 40.2 - - + +
106A ARG* 4.6 0.7 - - - +
54B TYR* 2.7 32.5 + - + +
55B ASN* 3.4 28.0 - - - +
57B GLU* 1.3 73.1 - - - +
59B LEU* 1.3 65.2 + - + +
61B LEU* 3.5 25.0 + - - +
66B ARG* 4.7 10.6 - - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.1 19.4 + - + +
56B ILE* 3.0 7.9 + - + +
58B ILE* 1.3 75.7 - - + +
60B ARG* 1.3 55.7 + - - +
61B LEU 2.8 24.1 + - - +
36X GLU* 3.6 33.4 - - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ILE* 2.8 30.4 + - + +
57B GLU* 2.8 52.4 + - - +
59B LEU* 1.3 74.3 - - - +
61B LEU* 1.3 63.4 + - + +
62B PRO* 3.7 6.4 - - - +
24F PHE* 4.9 5.5 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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