Contacts of the helix formed by residues 37 - 75 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 3.6 0.8 - - - -
36A ARG* 1.3 85.3 + - - +
38A LEU* 1.3 65.9 + - - +
39A THR* 3.6 7.6 + - - -
40A GLY* 2.9 32.4 + - - -
41A VAL* 2.9 23.6 + - - +
115A GLN* 3.4 17.2 - - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 1.3 77.3 - - - +
39A THR* 1.3 63.6 + - - +
41A VAL* 3.3 1.7 + - - +
42A GLN* 2.9 45.2 + - - +
112A LEU* 3.7 22.9 - - + -
115A GLN* 3.6 31.8 + - + +
116A GLN* 4.2 7.0 - - + -
119A ALA* 4.2 12.3 - - + -
10C GLN* 3.9 7.4 - - - +
13C ARG* 3.5 40.4 - - - +
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 3.4 7.8 + - - +
38A LEU* 1.3 77.8 - - - +
40A GLY* 1.3 56.9 + - - +
42A GLN* 3.2 17.6 + - - +
43A ASN* 2.9 47.3 + - - +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY* 4.4 8.5 - - - -
36A ARG 4.9 1.3 - - - -
37A ASP* 2.9 22.6 + - - -
39A THR* 1.3 77.3 - - - +
41A VAL* 1.3 61.2 + - - +
43A ASN* 3.3 10.2 + - - +
44A LEU* 3.1 28.1 + - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 3.1 25.1 - - - +
35A GLY* 4.2 2.5 - - - -
37A ASP 2.9 15.0 + - - +
38A LEU* 3.9 4.9 - - - +
40A GLY* 1.3 72.6 - - - +
42A GLN* 1.3 66.4 + - - +
44A LEU* 3.1 5.0 + - - +
45A ARG* 2.9 27.5 + - + +
108A LEU* 3.6 28.5 - - + +
111A SER* 3.1 15.5 - - - +
112A LEU* 3.7 22.0 - - + +
115A GLN* 3.5 17.7 - - + -
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 2.9 39.2 + - + +
39A THR* 3.5 27.6 + - - +
41A VAL* 1.3 79.0 - - - +
43A ASN* 1.3 62.8 + - - +
45A ARG* 3.4 7.9 + - - +
46A LYS* 3.2 26.8 + - - +
112A LEU* 4.0 11.6 - - + +
116A GLN* 5.6 0.3 + - - -
10C GLN* 4.1 15.2 - - - +
14C ASP* 5.3 1.0 - - - +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 2.9 35.3 + - - +
40A GLY* 3.6 10.8 - - - +
41A VAL 3.2 0.2 - - - -
42A GLN* 1.3 79.4 - - - +
44A LEU* 1.3 64.3 + - + +
46A LYS* 3.3 13.4 + - - +
47A LYS* 3.0 22.4 + - - +
50A ARG* 5.0 1.0 + - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 3.5 30.1 - - + +
34A TYR* 3.5 9.2 - - - +
35A GLY* 3.3 36.8 - - - +
40A GLY 3.1 15.0 + - - +
41A VAL 3.1 5.8 + - - +
43A ASN* 1.3 78.4 - - + +
45A ARG* 1.3 57.3 + - - +
47A LYS* 3.3 22.3 + - + +
48A HIS* 2.8 29.3 + - - +
104A ARG* 4.2 14.9 + - - +
108A LEU* 4.0 14.5 - - + +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 2.9 20.8 + - + +
42A GLN* 3.8 6.7 - - - +
44A LEU* 1.3 72.6 - - - +
46A LYS* 1.3 61.1 + - - +
48A HIS* 3.2 6.8 + - - +
49A LYS* 2.9 68.3 + - - +
108A LEU* 3.9 34.2 - - + +
109A GLU* 3.7 38.4 + - - +
112A LEU* 4.0 31.3 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN 3.2 16.2 + - - +
43A ASN* 3.3 16.6 + - - +
45A ARG* 1.3 75.8 - - - +
47A LYS* 1.3 63.7 + - - +
49A LYS* 3.2 12.0 + - + +
50A ARG* 3.1 43.2 + - - +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 5.9 7.6 - - - +
43A ASN 3.0 13.0 + - - +
44A LEU* 3.5 25.7 - - + +
46A LYS* 1.3 77.8 - - - +
48A HIS* 1.3 62.0 + - - +
50A ARG* 3.2 32.0 + - - +
51A LEU* 3.1 19.6 + - - +
104A ARG* 6.2 0.7 - - - +
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.7 2.2 - - + +
44A LEU 2.8 20.1 + - - +
45A ARG* 3.2 5.8 + - - +
47A LYS* 1.3 73.7 - - - +
49A LYS* 1.3 59.8 + - + +
51A LEU* 3.0 24.4 + - + +
52A GLU* 2.9 60.9 + - - +
101A ALA* 3.0 36.4 + - - -
104A ARG* 4.0 25.3 + - + +
105A GLY* 3.5 22.3 - - - -
108A LEU* 3.8 14.8 - - + -
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 2.9 58.5 + - - +
46A LYS* 3.2 10.5 + - + +
48A HIS* 1.3 78.4 - - + +
50A ARG* 1.3 61.6 + - + +
52A GLU* 3.4 20.1 + - - +
53A ALA* 3.2 21.8 + - - +
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Residues in contact with ARG 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN 5.0 1.2 + - - -
46A LYS* 3.1 41.3 + - - +
47A LYS* 3.4 38.8 - - - +
48A HIS 3.2 0.4 - - - -
49A LYS* 1.3 75.9 - - + +
51A LEU* 1.3 62.6 + - - +
53A ALA* 3.3 8.2 + - - +
54A GLU* 3.1 20.7 + - - +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 4.3 16.4 - - + -
28A LEU* 4.3 25.1 - - + -
29A VAL* 3.6 34.3 - - + +
47A LYS 3.1 11.1 + - - +
48A HIS* 3.0 28.1 + - + +
50A ARG* 1.3 75.4 - - - +
52A GLU* 1.3 62.9 + - - +
54A GLU* 3.0 12.9 + - + +
55A LEU* 2.9 42.6 + - + +
101A ALA* 4.3 5.8 - - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 2.9 47.9 + - + +
49A LYS* 3.8 22.4 - - - +
50A ARG 3.3 0.2 - - - -
51A LEU* 1.3 82.1 - - + +
53A ALA* 1.3 57.2 + - - +
55A LEU* 3.3 11.0 + - + +
56A ALA* 3.0 26.9 + - - +
101A ALA* 4.3 10.2 - - + +
102A ALA* 5.0 3.8 - - - -
105A GLY* 4.9 2.8 - - - -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS 3.2 13.2 + - - +
50A ARG* 3.6 11.4 - - - +
51A LEU 3.1 0.4 - - - -
52A GLU* 1.3 75.0 - - - +
54A GLU* 1.3 61.0 + - - +
56A ALA* 3.3 8.7 + - - +
57A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TRP* 3.0 34.2 + - + +
25A LYS* 3.1 25.0 + - + -
50A ARG 3.1 12.0 + - - +
51A LEU* 3.0 15.5 + - + +
53A ALA* 1.3 74.8 - - - +
55A LEU* 1.3 64.4 + - - +
57A ALA* 3.1 16.6 + - + +
58A HIS* 3.2 21.4 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.4 27.8 - - + -
25A LYS* 4.0 11.9 - - + -
51A LEU* 2.9 26.5 + - + +
52A GLU* 3.6 12.6 - - + +
53A ALA 3.3 0.2 - - - -
54A GLU* 1.3 76.7 - - - +
56A ALA* 1.3 62.9 + - - +
58A HIS* 3.1 11.4 + - - -
59A GLU* 3.1 12.7 + - - +
94A TRP* 3.7 18.2 - - + -
97A LEU* 3.7 26.7 - - + -
98A LYS* 4.7 14.8 - - + -
101A ALA* 3.9 28.0 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU 3.0 14.1 + - - +
53A ALA* 3.5 11.7 - - - +
55A LEU* 1.3 75.8 - - - +
57A ALA* 1.3 61.5 + - - +
59A GLU* 3.3 34.6 + - - +
60A PRO* 3.5 5.2 - - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 2.9 13.5 + - - +
54A GLU* 3.1 14.3 + - + +
56A ALA* 1.3 79.2 - - - +
58A HIS* 1.3 62.9 + - + +
59A GLU 3.4 0.2 - - - -
60A PRO* 3.4 17.5 - - - +
61A ALA* 5.6 0.3 - - - +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 2.9 29.3 + - - +
21A TRP* 3.5 64.3 + + + -
54A GLU* 3.2 23.9 + - + +
55A LEU 3.1 5.0 + - - +
57A ALA* 1.3 78.8 - - + +
59A GLU* 1.3 67.0 + - - +
60A PRO* 3.3 3.6 - - - -
61A ALA* 3.1 9.1 + - - +
62A ILE* 3.0 28.7 + - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.1 7.4 + - - +
56A ALA* 3.3 27.1 + - - +
58A HIS* 1.3 75.0 - - - +
60A PRO* 1.3 63.5 - - + +
62A ILE* 3.1 9.8 + - - +
63A GLN* 2.9 29.6 + - - +
94A TRP* 3.7 28.3 - - + +
98A LYS* 4.6 8.7 + - - +
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Residues in contact with PRO 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA 3.5 6.3 - - - +
57A ALA 3.4 18.6 - - - +
58A HIS 3.3 1.3 - - - -
59A GLU* 1.3 96.0 - - + +
61A ALA* 1.3 58.9 + - + +
63A GLN* 3.3 7.8 + - + +
64A SER* 2.9 31.7 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.5 25.1 - - + +
57A ALA 5.6 0.2 - - - +
58A HIS* 3.1 13.0 + - - +
60A PRO* 1.3 81.7 - - + +
62A ILE* 1.3 62.6 + - - +
64A SER* 3.3 8.7 + - - -
65A VAL* 3.3 26.6 + - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.7 26.2 - - + +
21A TRP* 4.7 2.9 - - + -
22A ILE* 4.2 15.3 - - + -
58A HIS 3.0 25.1 + - - +
59A GLU* 3.3 9.4 - - - +
61A ALA* 1.3 77.4 - - - +
63A GLN* 1.3 62.8 + - - +
65A VAL* 3.2 15.0 + - - +
66A LEU* 3.2 20.0 + - + +
90A PHE* 3.8 32.7 - - + -
94A TRP* 4.0 44.9 - - + +
----------------------------------------------------------
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU 2.9 15.1 + - - +
60A PRO* 3.7 8.1 - - + +
62A ILE* 1.3 74.7 - - - +
64A SER* 1.3 59.9 + - - +
66A LEU* 3.3 23.8 + - - +
67A ASP* 2.6 68.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO 2.9 20.6 + - - -
61A ALA* 3.6 9.9 - - - -
62A ILE 3.2 0.4 - - - -
63A GLN* 1.3 76.9 - - - +
65A VAL* 1.3 58.7 - - - +
67A ASP* 3.4 7.7 + - - +
68A THR* 2.9 34.5 + - - -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.2 27.3 - - + +
14A ASP* 4.0 29.6 - - + +
15A MET* 3.9 20.4 - - + +
18A GLU* 4.7 3.1 - - + -
61A ALA 3.3 15.5 - - - +
62A ILE 3.2 8.2 + - - +
64A SER* 1.3 76.5 - - - +
66A LEU* 1.3 58.8 + - - +
68A THR* 4.5 4.0 - - - -
69A GLY* 2.8 23.6 + - - -
87A LEU* 4.0 2.4 - - + +
90A PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.2 21.6 + - + +
63A GLN* 3.3 30.0 + - - +
65A VAL* 1.3 74.5 - - - +
67A ASP* 1.3 60.0 + - - +
69A GLY* 3.2 1.4 + - - -
70A LYS* 2.8 29.1 + - - +
87A LEU* 4.0 15.8 - - + +
90A PHE* 3.8 22.4 - - + -
91A VAL* 3.5 33.2 - - + -
94A TRP* 5.7 5.2 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 2.6 54.2 + - - +
64A SER* 3.8 7.0 - - - +
66A LEU* 1.3 77.4 - - - +
68A THR* 1.3 61.6 + - - +
70A LYS* 3.4 13.0 + - - +
71A LYS* 3.1 22.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.2 22.1 - - + +
11A PHE* 3.7 31.0 - - + -
64A SER* 2.9 21.2 + - - -
65A VAL* 3.8 4.3 - - - -
67A ASP* 1.3 73.6 - - - +
69A GLY* 1.3 66.1 + - - +
71A LYS* 3.3 6.5 + - - +
72A LEU* 3.0 29.5 + - + +
----------------------------------------------------------
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.6 15.0 - - - -
65A VAL 2.8 16.3 + - - -
66A LEU 3.6 0.4 - - - -
68A THR* 1.3 79.1 - - - +
70A LYS* 1.3 60.5 + - - +
72A LEU* 3.3 5.6 + - - +
73A SER* 3.0 24.6 + - - -
83A ILE* 4.2 2.2 - - - +
87A LEU* 3.5 26.3 - - - +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 2.8 15.6 + - - +
67A ASP* 3.7 11.2 - - - +
68A THR 3.2 0.4 - - - -
69A GLY* 1.3 77.5 - - - +
71A LYS* 1.3 60.1 + - - +
73A SER* 3.3 5.8 + - - -
74A ASP* 2.9 57.1 + - - +
87A LEU* 4.2 3.1 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.5 23.1 - - + +
67A ASP 3.1 13.9 + - - +
68A THR* 3.3 6.9 + - - +
70A LYS* 1.3 81.9 - - - +
72A LEU* 1.3 63.1 + - + +
74A ASP* 3.4 6.1 + - + +
75A ASP* 3.0 53.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.2 20.2 - - + -
8A VAL* 3.4 33.7 - - + -
11A PHE* 3.7 40.6 - - + -
68A THR* 3.0 27.5 + - + +
69A GLY* 3.6 5.6 - - - +
71A LYS* 1.3 77.1 - - - +
73A SER* 1.3 61.1 + - - +
75A ASP* 3.3 8.1 + - - +
77A THR* 2.9 41.5 + - - +
80A LYS* 5.3 0.2 - - - +
83A ILE* 4.2 17.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.0 17.5 + - - -
70A LYS* 3.6 6.7 - - - -
72A LEU* 1.3 75.6 - - - +
74A ASP* 1.3 68.3 + - - +
76A ASN 3.1 6.6 + - - -
80A LYS* 3.1 36.5 + - - +
83A ILE* 5.0 6.0 - - - +
84A GLN* 2.7 39.4 + - - -
87A LEU* 5.5 2.5 - - - -
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 2.9 52.2 + - - +
71A LYS* 4.0 5.9 - - - +
73A SER* 1.3 81.2 + - - +
75A ASP* 1.3 63.6 + - - +
76A ASN* 3.2 10.9 + - - +
80A LYS* 5.3 0.7 - - - +
----------------------------------------------------------
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.0 48.5 + - - +
72A LEU* 3.8 7.1 - - - +
73A SER 3.1 0.4 - - - -
74A ASP* 1.3 81.6 - - - +
76A ASN* 1.3 70.6 - - - +
77A THR* 3.2 8.2 + - - +
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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