Contacts of the helix formed by residues 28 - 71 (chain E) in PDB entry 3RK3
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 PRO 28 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LYS* 3.4 9.0 - - - -
27E LEU* 1.3 91.6 - - - +
29E ASP* 1.3 71.0 + - - +
30E ALA 3.5 0.7 - - - -
31E ALA* 3.2 23.4 - - + +
32E LYS* 3.3 33.6 + - - +
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LYS 4.8 7.9 - - - +
27E LEU* 3.2 3.1 - - + -
28E PRO* 1.3 93.7 - - - +
30E ALA* 1.3 54.4 + - - +
31E ALA 2.9 1.6 - - - -
32E LYS* 2.4 43.5 + - + +
33E LYS* 2.6 38.5 + - + +
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 3.8 33.2 + - + +
28E PRO 3.5 0.4 - - - -
29E ASP* 1.3 77.6 - - - +
31E ALA* 1.3 56.2 + - - +
33E LYS* 3.7 25.0 - - + +
34E PHE* 3.1 30.5 + - - +
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU 4.7 1.9 + - - +
28E PRO* 3.2 19.1 + - + +
29E ASP 2.9 0.6 - - - -
30E ALA* 1.3 78.8 - - - +
32E LYS* 1.3 58.8 + - + +
34E PHE* 4.5 2.1 - - - +
35E GLU* 3.0 33.3 + - - +
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E PRO* 3.3 44.7 + - - +
29E ASP* 2.4 31.4 + - + +
31E ALA* 1.3 72.1 - - + +
33E LYS* 1.3 57.6 + - + -
35E GLU* 4.2 5.1 - - - +
36E GLU* 2.7 43.6 + - - +
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU* 4.3 13.5 - - - +
29E ASP* 2.6 26.8 + - + +
30E ALA* 3.7 36.0 - - + +
32E LYS* 1.3 73.7 - - - +
34E PHE* 1.3 58.8 + - + +
36E GLU* 3.4 10.8 + - - +
37E ALA* 3.1 23.8 + - - +
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Residues in contact with PHE 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA 3.1 15.4 + - - +
31E ALA* 4.5 2.0 - - - +
33E LYS* 1.3 78.1 - - + +
35E GLU* 1.3 62.4 + - - +
37E ALA* 3.5 14.3 - - + +
38E GLN* 3.1 44.4 + - + +
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ALA* 3.0 23.6 + - - +
32E LYS* 4.2 5.6 - - - +
34E PHE* 1.3 78.0 - - - +
36E GLU* 1.3 63.3 + - + +
38E GLN* 3.5 7.5 + - + +
39E GLU* 3.2 38.7 + - + +
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LYS* 2.7 37.9 + - - +
33E LYS* 3.5 9.7 - - - +
35E GLU* 1.3 76.8 - - + +
37E ALA* 1.3 63.5 + - - +
39E GLU* 3.6 7.8 + - - +
40E ALA* 3.2 18.5 + - - +
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LYS 3.1 13.3 + - - +
34E PHE* 3.5 23.6 - - + +
35E GLU 3.4 0.2 - - - -
36E GLU* 1.3 75.8 - - - +
38E GLN* 1.3 54.5 + - - +
40E ALA* 2.7 34.3 + - - +
41E LEU* 3.0 13.6 + - + +
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Residues in contact with GLN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E PHE* 3.1 37.8 + - + +
35E GLU* 3.7 9.9 - - + +
36E GLU 3.3 0.4 - - - -
37E ALA* 1.3 75.6 - - - +
39E GLU* 1.3 58.4 + - + +
41E LEU* 3.3 30.4 + - - +
42E ARG* 3.0 32.4 + - + +
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Residues in contact with GLU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLU* 3.2 31.0 + - + +
36E GLU* 4.1 6.2 - - - +
37E ALA 3.3 0.2 - - - -
38E GLN* 1.3 75.4 - - + +
40E ALA* 1.3 60.7 + - - +
42E ARG* 3.6 20.2 + - + +
43E GLN* 2.9 43.8 + - - +
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLU 3.2 13.1 + - - +
37E ALA* 2.7 18.0 + - - +
39E GLU* 1.3 76.8 - - - +
41E LEU* 1.3 58.8 + - + +
43E GLN* 3.5 16.0 + - - +
44E ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ALA* 3.0 17.7 + - + +
38E GLN* 3.4 34.5 - - - +
40E ALA* 1.3 77.3 - - + +
42E ARG* 1.3 65.6 + - - +
44E ALA* 3.3 8.1 + - + +
45E GLU* 3.3 33.3 + - - +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLN* 3.0 24.1 + - + +
39E GLU* 3.4 24.2 + - + +
41E LEU* 1.3 74.6 - - - +
43E GLN* 1.3 61.8 + - + +
45E GLU* 5.9 0.2 - - - -
46E GLU* 3.2 42.2 + - - +
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Residues in contact with GLN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLU* 2.9 32.6 + - + +
40E ALA* 3.6 15.0 - - - +
42E ARG* 1.3 73.7 - - + +
44E ALA* 1.3 68.7 + - - +
47E GLU* 3.0 52.3 + - - +
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Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA 3.0 14.8 + - - +
41E LEU* 3.3 13.2 + - + +
43E GLN* 1.3 78.6 - - - +
45E GLU* 1.3 65.4 + - + +
47E GLU* 4.2 1.6 - - - +
48E ARG* 3.0 34.7 + - - +
51E LYS* 5.4 1.4 + - - -
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 3.3 19.8 + - - +
42E ARG* 5.9 0.4 - - - -
44E ALA* 1.3 82.9 - - + +
46E GLU* 1.3 60.3 + - - +
48E ARG* 3.8 23.7 + - - +
49E LYS* 2.9 56.0 + - - +
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Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ARG* 3.2 29.9 + - - +
45E GLU* 1.3 74.3 - - - +
47E GLU* 1.3 63.6 + - + +
49E LYS* 3.7 13.6 - - + +
50E ALA* 3.3 19.4 + - - +
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLN* 3.0 47.9 + - - +
44E ALA* 4.9 0.9 - - - -
46E GLU* 1.3 75.2 - - + +
48E ARG* 1.3 60.4 + - - +
49E LYS 3.1 1.3 - - - -
50E ALA* 2.8 10.4 + - - +
51E LYS* 2.8 57.3 + - - +
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ALA* 3.0 29.6 + - - +
45E GLU* 3.9 25.2 + - - +
47E GLU* 1.3 76.4 - - - +
49E LYS* 1.3 60.4 + - + +
51E LYS* 4.1 14.2 - - + +
52E TYR* 3.3 23.0 + - + +
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Residues in contact with LYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLU* 2.9 48.7 + - - +
46E GLU* 3.7 12.2 - - + +
47E GLU 3.1 0.2 - - - -
48E ARG* 1.3 75.0 - - + +
50E ALA* 1.3 63.6 + - - +
52E TYR* 3.5 7.5 + - - +
53E ALA* 3.2 20.8 + - - +
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Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLU 3.3 11.6 + - - +
47E GLU* 2.8 16.4 + - - +
49E LYS* 1.3 74.8 - - - +
51E LYS* 1.3 61.9 + - + +
53E ALA* 3.2 17.1 + - - +
54E LYS* 3.3 19.4 + - - +
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ALA 5.4 1.0 + - - -
47E GLU* 2.8 50.5 + - + +
48E ARG* 4.1 12.2 - - - +
50E ALA* 1.3 73.8 - - + +
52E TYR* 1.3 62.3 + - - +
54E LYS* 3.6 5.7 + - - +
55E MET* 3.3 29.9 + - + +
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Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 5.2 6.8 + - - -
229B MET* 5.7 6.1 - - + +
232B ARG* 6.1 2.5 - - - -
48E ARG* 3.3 17.1 + - + +
49E LYS* 3.8 7.2 - - - +
50E ALA 3.3 0.8 - - - -
51E LYS* 1.3 75.8 - - - +
53E ALA* 1.3 68.5 + - - +
55E MET* 4.1 6.0 - - + +
56E GLU* 3.2 47.1 + - + +
59E ARG* 5.5 5.1 + - - -
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LYS 3.2 12.8 + - - +
50E ALA* 3.2 13.4 + - - +
52E TYR* 1.3 82.6 - - - +
54E LYS* 1.3 63.4 + - + +
56E GLU* 3.5 5.3 - - - +
57E ALA* 3.3 21.0 + - - +
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Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ALA* 3.3 14.5 + - - +
51E LYS* 4.2 5.8 - - - +
52E TYR 3.4 0.2 - - - -
53E ALA* 1.3 80.3 - - + +
55E MET* 1.3 61.2 + - + +
57E ALA* 3.4 6.6 + - - +
58E GLU* 2.9 37.2 + - - +
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Residues in contact with MET 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LYS* 3.3 20.0 + - + +
52E TYR* 4.1 7.6 - - + +
54E LYS* 1.3 74.6 - - + +
56E GLU* 1.3 66.3 + - - +
58E GLU* 3.5 34.6 - - + +
59E ARG* 2.9 34.9 + - + +
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Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN 5.7 0.9 - - - +
60A LEU* 4.9 1.8 - - - +
52E TYR* 3.2 45.0 + - + +
53E ALA* 3.5 7.2 - - - +
55E MET* 1.3 79.8 - - - +
57E ALA* 1.3 65.2 + - - +
59E ARG* 3.6 29.8 + - - +
60E GLU* 2.9 19.7 + - + +
63E ARG* 3.1 32.6 + - - +
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Residues in contact with ALA 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ALA 3.3 10.9 + - - +
54E LYS* 3.7 9.9 - - - +
56E GLU* 1.3 80.4 - - - +
58E GLU* 1.3 57.8 + - - +
60E GLU* 3.3 10.2 + - - +
61E ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LYS* 2.9 19.7 + - - +
55E MET* 3.5 43.3 - - + +
56E GLU 3.2 0.2 - - - -
57E ALA* 1.3 74.6 - - + +
59E ARG* 1.3 63.0 + - + +
61E ALA* 3.3 22.2 - - + +
62E VAL* 3.4 13.8 + - + +
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Residues in contact with ARG 59 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.6 23.8 + - - +
58A GLN 5.0 0.6 + - - -
60A LEU* 2.7 29.5 + - - -
229B MET* 3.2 33.6 - - - +
52E TYR* 5.5 4.8 - - - -
55E MET* 2.9 21.6 + - + +
56E GLU* 3.6 31.9 + - - +
58E GLU* 1.3 77.0 - - + +
60E GLU* 1.3 58.7 + - - +
61E ALA 3.1 1.6 - - - -
62E VAL* 3.1 12.0 + - + +
63E ARG* 2.7 55.4 + - - +
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Residues in contact with GLU 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 4.2 13.0 + - - -
56E GLU* 2.9 8.8 + - + +
57E ALA* 3.4 13.9 - - - +
59E ARG* 1.3 75.9 - - - +
61E ALA* 1.3 59.0 + - - +
63E ARG* 3.3 43.4 + - - +
64E GLN* 3.0 38.5 + - - +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ALA 3.0 10.1 + - - +
58E GLU* 3.3 20.0 - - + +
60E GLU* 1.3 75.1 - - - +
62E VAL* 1.3 55.0 + - + +
64E GLN* 3.2 5.3 + - - +
65E GLY* 2.7 32.9 + - - -
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Residues in contact with VAL 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B MET* 6.3 2.9 - - - -
222B LEU* 5.0 15.7 - - + -
58E GLU* 3.4 13.6 + - + +
59E ARG* 3.1 15.6 + - + +
61E ALA* 1.3 78.7 - - + +
63E ARG* 1.3 67.5 + - + +
65E GLY* 3.7 1.5 - - - -
66E ILE* 3.1 35.2 + - + +
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.1 28.8 - - + +
57A ASP* 3.3 29.6 + - - +
58A GLN* 3.3 44.2 + - - +
222B LEU* 6.0 2.5 - - + -
56E GLU* 3.1 30.9 + - - +
59E ARG* 2.7 21.4 + - + +
60E GLU* 3.3 56.2 + - - +
62E VAL* 1.3 81.5 - - + +
64E GLN* 1.3 63.2 + - - +
66E ILE* 3.5 6.4 - - - +
67E ARG* 3.0 24.8 + - - +
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Residues in contact with GLN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU* 3.0 29.0 + - - +
61E ALA* 3.7 5.2 - - - +
63E ARG* 1.3 78.3 - - - +
65E GLY* 1.3 67.8 + - - +
67E ARG* 2.7 46.6 + - - +
68E ASP* 2.9 41.4 + - - +
72E ILE 5.5 0.2 + - - -
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Residues in contact with GLY 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ALA 2.7 20.1 + - - -
62E VAL* 3.2 3.5 + - - -
64E GLN* 1.3 73.3 - - - +
66E ILE* 1.3 62.4 + - - +
68E ASP* 3.5 11.8 + - - +
69E LYS* 3.1 17.4 + - - +
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.0 26.2 - - + -
54A LEU* 4.1 16.4 - - + -
218B ASP* 5.0 17.5 - - + +
222B LEU* 5.3 9.4 - - + -
62E VAL* 3.1 25.0 + - + +
63E ARG* 3.5 11.0 - - - +
64E GLN 3.1 0.6 - - - -
65E GLY* 1.3 72.1 - - - +
67E ARG* 1.3 82.0 + - - +
68E ASP 3.0 2.2 - - - -
69E LYS* 2.7 35.2 + - + +
70E TYR* 3.2 16.8 + - + -
72E ILE* 6.2 1.1 - - + -
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Residues in contact with ARG 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.9 16.2 + - - -
54A LEU* 3.5 34.0 - - + +
55A GLU* 5.8 4.6 - - - +
58A GLN* 4.6 16.6 + - - +
63E ARG* 3.0 16.3 + - - +
64E GLN* 2.7 46.9 + - - +
66E ILE* 1.3 86.0 - - - +
68E ASP* 1.3 50.2 + - - +
70E TYR* 3.4 1.5 + - - +
71E GLY* 2.6 33.8 + - - -
72E ILE* 3.2 40.7 + - + +
73E LYS* 3.4 27.1 + - - +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLN* 2.9 44.5 + - - +
65E GLY* 3.6 10.0 + - - +
67E ARG* 1.3 71.8 - - - +
69E LYS* 1.3 64.6 + - - +
70E TYR 2.8 7.4 + - - -
71E GLY* 3.0 12.8 + - - +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLU* 4.2 7.2 - - - +
214B ASP* 4.0 19.6 + - - -
218B ASP* 3.1 25.6 + - - +
65E GLY 3.1 6.1 + - - +
66E ILE* 2.7 32.3 + - + +
68E ASP* 1.3 74.0 - - - +
70E TYR* 1.3 89.9 + - + +
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Residues in contact with TYR 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 3.8 33.9 + - + +
50A VAL* 4.6 13.7 - - + -
211B GLU* 3.4 30.1 - - - -
214B ASP* 3.2 25.7 - - + +
215B MET* 3.6 31.6 - - + -
218B ASP* 2.6 33.8 + - + -
66E ILE* 3.2 29.1 + - + +
67E ARG 4.3 1.1 - - - +
68E ASP 2.9 0.6 - - - -
69E LYS* 1.3 103.6 - - + +
71E GLY* 1.3 65.9 + - - +
72E ILE* 3.6 7.9 - - + -
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Residues in contact with GLY 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.5 1.0 - - - -
67E ARG 2.6 15.9 + - - -
68E ASP* 3.0 11.0 + - - -
70E TYR* 1.3 76.2 - - - +
72E ILE* 1.3 63.8 + - - +
73E LYS* 5.5 1.0 - - - +
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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