Contacts of the helix formed by residues 37 - 75 (chain B) in PDB entry 1CUN
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 ASP 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 3.6 0.4 - - - -
36B ARG* 1.3 83.7 - - - +
38B LEU* 1.3 64.6 + - - +
39B THR* 3.6 8.5 + - - -
40B GLY* 2.9 22.9 + - - -
41B VAL* 3.0 23.9 + - - +
115B GLN* 3.4 15.9 - - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 4.0 4.5 - - - +
13A ARG* 3.7 36.8 - - - +
37B ASP* 1.3 75.1 - - - +
39B THR* 1.3 64.6 + - - +
41B VAL* 3.1 2.5 + - + +
42B GLN* 3.0 50.6 + - - +
112B LEU* 3.5 32.3 - - + +
115B GLN* 3.7 29.0 + - + +
116B GLN* 4.0 10.5 - - + +
119B ALA* 4.4 12.1 - - + -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 3.4 8.1 + - - -
38B LEU* 1.3 76.9 - - - +
40B GLY* 1.3 58.2 - - - +
42B GLN* 3.2 16.9 + - - +
43B ASN* 2.9 46.6 + - - +
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY* 4.4 10.5 - - - -
36B ARG 5.0 1.1 - - - -
37B ASP* 2.9 22.6 + - - -
39B THR* 1.3 77.7 - - - +
41B VAL* 1.3 60.3 + - - +
43B ASN* 3.2 10.7 + - - +
44B LEU* 3.1 26.6 + - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 3.7 12.8 - - - +
35B GLY* 4.4 2.0 - - - -
37B ASP 3.0 17.2 + - - +
38B LEU 3.1 3.8 + - - +
40B GLY* 1.3 74.2 - - - +
42B GLN* 1.3 64.1 + - - +
44B LEU* 3.1 5.5 + - - +
45B ARG* 2.9 28.3 + - + +
108B LEU* 3.6 16.4 - - + +
111B SER* 3.5 16.8 - - - +
112B LEU* 3.5 34.3 - - + +
115B GLN* 3.4 27.4 - - + -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 4.0 17.6 + - - +
14A ASP* 5.7 0.4 + - - -
38B LEU* 3.0 47.1 + - + +
39B THR* 3.6 19.6 + - - +
41B VAL* 1.3 76.6 - - - +
43B ASN* 1.3 61.3 + - - +
45B ARG* 3.3 8.8 + - - +
46B LYS* 3.2 38.6 + - - +
112B LEU* 4.0 11.5 - - + +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 2.9 34.5 + - - +
40B GLY* 3.6 10.8 - - - +
41B VAL 3.2 0.2 - - - -
42B GLN* 1.3 76.9 - - - +
44B LEU* 1.3 62.4 + - + +
46B LYS* 3.4 27.4 + - - +
47B LYS* 3.2 21.1 + - - +
50B ARG* 5.1 1.4 + - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 3.6 28.9 - - + +
34B TYR* 3.6 8.5 - - - +
35B GLY* 3.3 36.1 - - - +
40B GLY 3.1 15.2 + - - +
41B VAL* 3.1 6.2 + - - +
43B ASN* 1.3 76.3 - - + +
45B ARG* 1.3 60.3 + - - +
47B LYS* 3.4 19.2 + - + +
48B HIS* 2.8 28.6 + - - +
104B ARG* 4.1 15.2 + - - +
108B LEU* 4.0 14.9 - - + +
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Residues in contact with ARG 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 VAL* 2.9 21.2 + - + +
42B GLN* 3.8 6.7 - - - +
43B ASN 3.3 0.4 - - - -
44B LEU* 1.3 73.9 - - - +
46B LYS* 1.3 60.8 + - - +
48B HIS* 3.2 7.2 + - - +
49B LYS* 2.8 63.7 + - + +
105B GLY 5.2 0.2 + - - -
108B LEU* 4.0 30.9 - - + +
109B GLU* 3.2 39.4 + - - +
112B LEU* 3.9 34.8 - - - +
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Residues in contact with LYS 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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42B GLN* 3.2 31.8 + - - +
43B ASN* 3.4 33.0 + - - +
45B ARG* 1.3 75.8 - - - +
47B LYS* 1.3 62.6 + - - +
49B LYS* 3.4 11.1 + - + +
50B ARG* 3.2 40.9 + - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 6.1 5.5 - - - +
43B ASN 3.2 11.3 + - - +
44B LEU* 3.6 22.4 - - + +
46B LYS* 1.3 78.3 - - - +
48B HIS* 1.3 65.7 + - - +
50B ARG* 3.2 38.5 + - - +
51B LEU* 3.2 11.8 + - - +
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.1 14.1 - - + +
44B LEU 2.8 18.3 + - - +
45B ARG* 3.2 5.8 + - - +
47B LYS* 1.3 78.3 - - - +
49B LYS* 1.3 63.1 + - + +
51B LEU* 3.1 10.8 + - + +
52B GLU* 3.0 61.0 + - + +
101B ALA* 3.0 34.2 + - + -
104B ARG* 4.0 22.5 + - + +
105B GLY* 3.5 20.5 - - - -
108B LEU* 3.7 14.8 - - + -
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Residues in contact with LYS 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 ARG* 2.8 52.0 + - + +
46B LYS* 3.8 8.1 - - - +
47B LYS 3.3 0.2 - - - -
48B HIS* 1.3 77.2 - - + +
50B ARG* 1.3 62.6 + - + +
52B GLU* 3.2 20.3 + - - +
53B ALA* 3.0 22.9 + - - +
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Residues in contact with ARG 50 (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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43B ASN 5.1 1.6 + - - -
46B LYS* 3.2 32.1 + - - +
47B LYS* 3.5 37.6 + - - +
48B HIS 3.2 0.6 - - - -
49B LYS* 1.3 77.1 - - + +
51B LEU* 1.3 62.4 + - - +
53B ALA* 3.3 8.4 + - - +
54B GLU* 3.1 32.9 + - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.1 33.4 - - + +
28B LEU* 4.8 13.2 - - + -
29B VAL* 3.8 30.3 - - + -
47B LYS 3.2 8.0 + - - +
48B HIS* 3.1 16.9 + - + +
50B ARG* 1.3 78.4 - - - +
52B GLU* 1.3 67.5 + - - +
54B GLU* 3.1 16.0 + - + +
55B LEU* 3.0 46.5 + - + +
97B LEU* 5.6 2.0 - - + -
101B ALA* 4.2 5.8 - - + -
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Residues in contact with GLU 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 HIS* 3.0 49.1 + - + +
49B LYS* 3.2 24.7 + - - +
51B LEU* 1.3 78.6 - - + +
53B ALA* 1.3 62.7 + - - +
55B LEU* 3.3 12.1 + - + +
56B ALA* 3.2 21.1 + - - +
101B ALA* 4.4 9.5 - - + +
102B ALA* 5.1 3.8 - - - -
105B GLY* 4.7 3.5 - - - -
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Residues in contact with ALA 53 (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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49B LYS 3.0 13.4 + - - +
50B ARG* 3.6 10.8 - - - +
51B LEU 3.2 0.4 - - - -
52B GLU* 1.3 74.8 - - - +
54B GLU* 1.3 60.9 + - + +
56B ALA* 3.3 7.9 + - - +
57B ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 4.3 12.6 + - + -
25B LYS* 3.5 31.3 + - - -
50B ARG* 3.1 25.4 + - - +
51B LEU* 3.1 18.8 + - + +
53B ALA* 1.3 74.3 - - - +
55B LEU* 1.3 67.5 + - + +
57B ALA* 3.2 8.3 + - - +
58B HIS* 3.0 25.5 + - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.7 23.6 - - + -
25B LYS* 4.8 4.9 - - + -
51B LEU* 3.0 32.1 + - + +
52B GLU* 3.6 11.9 - - + +
53B ALA 3.2 0.2 - - - -
54B GLU* 1.3 77.9 - - + +
56B ALA* 1.3 61.6 + - - +
58B HIS* 3.1 11.8 + - - +
59B GLU* 3.2 16.7 + - - +
94B TRP* 3.7 15.2 - - + -
97B LEU* 3.8 29.2 - - + -
98B LYS* 4.7 13.9 - - + -
101B ALA* 3.9 28.5 - - + -
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Residues in contact with ALA 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 GLU 3.2 10.8 + - - +
53B ALA* 3.6 11.0 - - - +
55B LEU* 1.3 78.2 - - - +
57B ALA* 1.3 61.6 + - - +
58B HIS 3.3 0.5 + - - -
59B GLU* 3.4 23.7 + - - +
60B PRO* 3.8 4.0 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA 2.9 16.8 + - - +
54B GLU* 3.2 8.3 + - - +
56B ALA* 1.3 76.5 - - - +
58B HIS* 1.3 60.9 + - - +
60B PRO* 3.6 11.4 - - - +
61B ALA* 5.3 0.7 + - - +
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Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 2.7 39.4 + - - -
21B TRP* 3.5 59.2 + + + -
54B GLU 3.0 15.7 + - - +
55B LEU 3.1 4.9 + - - +
57B ALA* 1.3 77.9 - - - +
59B GLU* 1.3 65.0 + - - +
60B PRO* 3.3 3.1 - - - -
61B ALA* 2.9 25.4 + - + +
62B ILE* 3.2 19.0 + - - +
94B TRP* 4.5 2.5 - - + -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU 3.2 19.2 + - - +
56B ALA* 3.6 13.7 - - - +
58B HIS* 1.3 75.1 - - - +
60B PRO* 1.3 71.2 - - + +
62B ILE* 3.1 5.0 + - - +
63B GLN* 2.9 28.3 + - - +
94B TRP* 3.4 27.7 + - - -
98B LYS* 3.3 28.1 + - - -
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Residues in contact with PRO 60 (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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56B ALA 3.8 5.4 - - - +
57B ALA* 3.6 13.2 - - - +
58B HIS 3.4 4.7 - - - -
59B GLU* 1.3 95.8 - - + +
61B ALA* 1.3 55.0 + - - +
63B GLN* 3.4 6.7 + - + +
64B SER* 2.9 30.1 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.8 20.8 - - - +
57B ALA 5.7 0.2 - - - +
58B HIS* 2.9 24.9 + - + +
60B PRO* 1.3 76.3 - - - +
62B ILE* 1.3 67.3 + - - +
64B SER* 3.4 12.8 + - - -
65B VAL* 3.5 16.8 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.8 24.9 - - + +
22B ILE* 4.2 13.9 - - + -
58B HIS* 3.7 18.4 - - + +
59B GLU* 3.1 7.5 + - - +
61B ALA* 1.3 75.8 - - - +
63B GLN* 1.3 65.2 + - - +
65B VAL* 3.1 15.1 + - - +
66B LEU* 3.2 21.4 + - + +
90B PHE* 3.8 32.3 - - + -
94B TRP* 3.8 54.5 - - + +
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 2.9 20.1 + - - +
60B PRO* 3.7 8.3 - - + +
62B ILE* 1.3 78.4 - - - +
64B SER* 1.3 50.1 + - - +
66B LEU* 3.0 29.3 + - - +
67B ASP* 2.7 64.6 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO 2.9 17.8 + - - -
61B ALA* 3.6 10.3 - - - -
62B ILE 3.2 0.2 - - - -
63B GLN* 1.3 77.4 - - - +
65B VAL* 1.3 60.9 + - - +
67B ASP* 3.4 9.5 + - - +
68B THR* 3.1 28.1 + - - -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.4 26.0 - - + -
14B ASP* 4.1 26.2 - - + +
15B MET* 4.1 17.9 - - + +
18B GLU* 4.1 18.2 - - + +
61B ALA 3.5 12.8 + - - +
62B ILE 3.1 8.1 + - - +
64B SER* 1.3 73.8 - - - +
66B LEU* 1.3 62.5 + - - +
68B THR* 3.2 5.5 + - - -
69B GLY 2.9 25.3 + - - -
87B LEU* 4.8 0.7 - - + -
90B PHE* 3.7 21.8 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.5 21.5 - - + +
63B GLN* 3.0 36.7 + - - +
65B VAL* 1.3 78.1 - - - +
67B ASP* 1.3 62.1 + - - +
69B GLY* 3.3 1.7 + - - -
70B LYS* 3.1 22.2 + - - +
87B LEU* 4.1 16.8 - - + +
90B PHE* 3.6 29.6 - - + -
91B VAL* 3.7 28.5 - - + -
94B TRP* 5.8 2.9 - - + -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 2.7 53.2 + - - +
64B SER* 3.8 8.2 - - - +
65B VAL 3.2 0.2 - - - -
66B LEU* 1.3 72.6 - - - +
68B THR* 1.3 61.4 + - - +
70B LYS* 3.2 11.5 + - - +
71B LYS* 3.1 21.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 3.5 30.6 - - + +
11B PHE* 3.8 27.6 - - + -
64B SER* 3.1 19.7 + - - -
65B VAL* 3.6 4.9 - - - -
67B ASP* 1.3 76.0 - - - +
69B GLY* 1.3 59.4 + - - +
71B LYS* 3.2 8.7 + - - +
72B LEU* 2.9 28.9 + - + +
----------------------------------------------------------
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.6 23.0 - - - -
65B VAL 2.9 10.9 + - - -
66B LEU 3.7 1.6 - - - -
67B ASP 3.3 0.2 - - - -
68B THR* 1.3 77.9 - - - +
70B LYS* 1.3 55.3 + - - +
72B LEU* 3.4 6.9 + - - +
73B SER* 2.9 30.0 + - - -
83B ILE* 4.0 1.9 - - - +
87B LEU* 3.7 22.3 - - - +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU 3.1 13.6 + - - +
67B ASP* 3.2 13.4 + - - +
69B GLY* 1.3 72.6 - - - +
71B LYS* 1.3 57.7 + - - +
73B SER* 3.2 6.5 + - - -
74B ASP* 2.8 64.5 + - - +
87B LEU* 4.3 2.4 - - - +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 3.8 20.6 - - + -
67B ASP 3.1 13.6 + - - +
68B THR* 3.5 10.3 - - - +
70B LYS* 1.3 78.4 - - - +
72B LEU* 1.3 60.8 + - - +
74B ASP* 3.9 5.6 - - - +
75B ASP* 3.0 46.8 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 3.9 33.7 - - + -
8B VAL* 4.1 23.6 - - + -
11B PHE* 3.6 46.7 - - + -
68B THR* 2.9 22.1 + - + +
69B GLY* 3.6 4.3 - - - +
70B LYS 3.2 0.2 - - - -
71B LYS* 1.3 75.5 - - - +
73B SER* 1.3 61.7 + - - +
75B ASP* 3.5 3.0 + - - +
77B THR* 2.8 51.6 + - + +
80B LYS* 5.4 0.3 - - - +
83B ILE* 4.0 12.7 - - + +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 2.9 17.5 + - - -
70B LYS* 3.5 7.9 - - - -
72B LEU* 1.3 76.7 - - - +
74B ASP* 1.3 66.8 + - - +
76B ASN* 3.2 10.6 + - - -
80B LYS* 2.8 32.3 + - - +
83B ILE* 4.8 7.4 - - - +
84B GLN* 3.0 36.3 + - - +
87B LEU* 5.3 2.5 - - - -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 2.8 57.0 + - - +
71B LYS* 3.9 5.8 + - - +
73B SER* 1.3 74.3 + - - +
75B ASP* 1.3 61.3 - - - +
76B ASN* 3.0 20.6 + - - +
80B LYS* 4.9 1.8 + - - +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 5.4 1.7 - - - +
71B LYS* 3.0 38.8 + - - +
72B LEU* 3.5 0.9 + - - +
73B SER 3.3 0.6 - - - -
74B ASP* 1.3 78.6 - - - +
76B ASN* 1.3 70.5 + - - +
77B THR* 2.9 15.9 + - + +
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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) + - + + + + + -
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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