Contacts of the helix formed by residues 38 - 74 (chain D) in PDB entry 4O46
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 38 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D PRO 4.0 0.6 + - - -
37D LEU* 1.3 75.3 - - - +
39D ASN* 1.4 55.1 + - - +
40D GLU* 3.6 8.9 + - - +
41D GLU* 2.9 38.8 + - - +
42D ARG* 2.8 32.8 + - - +
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D SER* 1.4 72.8 - - - +
40D GLU* 1.4 59.3 + - - +
42D ARG* 2.8 40.8 + - - +
43D ASN* 2.8 34.9 + - - +
118D GLU* 4.4 13.0 + - - +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.5 1.6 - - - +
12D ARG* 2.7 50.8 + - - +
38D SER* 3.2 8.0 + - - +
39D ASN* 1.4 74.6 - - - +
41D GLU* 1.4 60.0 + - - +
43D ASN* 3.3 7.8 + - - +
44D LEU* 2.9 48.3 + - + +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ARG* 3.1 40.8 + - - -
8D VAL* 3.6 33.9 - - + +
27D MET* 3.2 23.0 - - + +
30D VAL* 4.6 0.7 - - - -
36D PRO 4.1 0.7 - - - +
37D LEU* 3.9 8.3 - - + -
38D SER* 2.9 37.4 + - - +
40D GLU* 1.4 74.3 - - + +
42D ARG* 1.3 64.3 + - - +
44D LEU* 3.2 4.3 + - - -
45D LEU* 3.1 21.8 + - - +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 4.0 13.2 + - + +
38D SER 2.8 20.8 + - - +
39D ASN* 2.8 44.8 + - - +
41D GLU* 1.3 72.7 - - - +
43D ASN* 1.3 64.0 + - - +
45D LEU* 3.7 4.9 + - - +
46D SER* 3.2 25.1 + - - -
118D GLU* 4.4 5.7 + - - +
119D SER* 3.4 27.1 + - - +
122D PHE* 3.4 50.0 - - + -
123D TYR* 3.4 31.9 - - + +
171D ILE* 3.5 27.8 - - - +
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ASN* 2.8 31.6 + - - +
40D GLU* 3.7 5.2 - - - +
42D ARG* 1.3 82.6 - - - +
44D LEU* 1.4 61.4 + - - +
46D SER* 3.3 4.6 + - - -
47D VAL* 2.9 40.9 + - + +
122D PHE* 4.0 22.6 - - - -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.8 30.7 - - + +
11D ALA* 4.7 0.9 - - + -
12D ARG* 4.2 23.3 - - + +
15D GLU* 3.7 15.5 - - - +
23D MET* 3.3 26.8 - - + +
27D MET* 3.8 18.8 - - + +
40D GLU* 2.9 39.2 + - + +
41D GLU* 3.2 12.1 + - - +
43D ASN* 1.4 75.7 - - - +
45D LEU* 1.4 56.1 + - - +
47D VAL* 4.7 0.9 - - - -
48D ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET* 3.7 28.6 - - + +
31D THR* 3.9 13.9 - - - +
37D LEU* 4.1 15.3 - - + -
41D GLU 3.1 15.9 + - - +
42D ARG 3.8 5.8 - - - +
44D LEU* 1.4 73.4 - - - +
46D SER* 1.3 64.9 + - - +
48D ALA* 3.4 2.6 + - - +
49D TYR* 3.1 54.6 + - + +
100D VAL* 6.0 1.8 - - + -
103D LEU* 4.4 8.7 - - + -
108D LEU* 3.6 29.8 - - + -
123D TYR* 4.9 2.9 - - + -
126D MET* 4.5 17.5 - - + -
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG 3.2 15.4 + - - -
43D ASN* 3.3 7.8 + - - -
45D LEU* 1.3 79.3 - - - +
47D VAL* 1.4 52.9 + - - +
49D TYR* 3.9 0.3 - - - -
50D LYS* 2.9 40.4 + - - +
122D PHE* 3.8 24.2 - - - -
125D LYS* 5.8 2.3 + - - -
126D MET* 4.2 21.9 - - - +
130D TYR* 4.1 2.9 + - - -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.5 26.5 - - - +
20D TYR* 4.5 3.4 - - + -
23D MET* 4.0 10.8 - - + -
43D ASN* 2.9 27.9 + - + +
44D LEU* 4.0 3.1 - - - +
46D SER* 1.4 69.9 - - - +
48D ALA* 1.3 67.0 + - - +
50D LYS* 3.4 5.4 + - - +
51D ASN* 2.9 45.0 + - - +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 4.0 3.7 - - - +
23D MET* 3.7 21.7 - - + -
24D ALA* 3.5 33.0 - - - +
27D MET* 4.9 0.4 - - + -
44D LEU 3.0 19.3 + - - +
45D LEU* 3.5 8.1 - - - +
47D VAL* 1.3 81.2 - - - +
49D TYR* 1.3 61.8 + - - +
51D ASN* 3.4 3.1 + - - +
52D VAL* 3.2 26.9 + - - +
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 3.8 33.4 + - + +
28D LYS* 3.6 20.1 - - - +
45D LEU* 3.1 46.0 + - + +
46D SER 5.1 0.2 - - - -
48D ALA* 1.3 76.4 - - - +
50D LYS* 1.4 60.0 + - - +
52D VAL* 3.8 5.5 - - + +
53D VAL* 2.9 33.8 + - - +
96D VAL* 4.0 15.9 - - + -
99D ASP* 2.7 33.4 + - + -
100D VAL* 3.3 33.2 - - + -
103D LEU* 3.8 13.1 - - + +
126D MET* 5.2 1.1 - - + -
130D TYR* 3.3 15.3 - - + +
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 2.9 24.9 + - - +
47D VAL* 3.7 6.3 - - - +
49D TYR* 1.4 74.7 - - - +
51D ASN* 1.3 56.7 + - - +
53D VAL* 3.6 4.0 - - - +
54D GLY* 2.8 32.8 + - - -
57D ARG* 4.1 15.3 - - - +
130D TYR* 3.2 9.7 + - + +
133D TYR* 3.3 30.5 - - + +
178D ASN* 6.3 0.2 - - - +
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Residues in contact with ASN 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.4 56.7 + - + -
47D VAL* 2.9 37.1 + - - +
48D ALA 3.7 0.7 - - - +
50D LYS* 1.3 77.0 - - - +
52D VAL* 1.4 63.0 + - - +
54D GLY* 4.7 1.1 - - - -
55D ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 3.4 26.5 - - + +
21D ASP* 3.5 26.7 - - - +
24D ALA* 4.2 9.4 - - + -
48D ALA 3.2 17.7 + - - +
49D TYR* 3.3 9.8 + - + +
51D ASN* 1.4 78.4 - - - +
53D VAL* 1.3 61.9 + - - +
55D ALA* 3.5 4.8 + - - +
56D ARG* 3.1 36.4 + - - +
96D VAL* 3.8 27.4 - - + -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TYR 2.9 20.1 + - - +
50D LYS* 3.6 7.9 - - + +
52D VAL* 1.3 73.2 - - - +
54D GLY* 1.3 64.3 + - - +
56D ARG* 3.0 8.3 + - - +
57D ARG* 2.9 35.9 + - + +
93D LEU* 4.0 19.3 - - + +
96D VAL* 3.9 17.7 - - + -
97D CYS* 3.9 28.0 - - - -
130D TYR* 3.7 17.7 - - + -
133D TYR* 3.9 20.6 - - + -
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Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS* 2.8 22.2 + - - -
51D ASN* 3.8 2.5 - - - -
52D VAL 3.3 0.2 - - - -
53D VAL* 1.3 78.0 - - - +
55D ALA* 1.3 54.4 + - - +
57D ARG* 3.5 14.4 - - - +
58D SER* 2.9 33.1 + - - -
61D ARG* 4.9 1.2 + - - -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 6.0 0.4 - - - -
51D ASN 3.1 12.7 + - - +
52D VAL* 3.5 11.4 - - - +
53D VAL 3.3 0.4 - - - -
54D GLY* 1.3 74.5 - - - +
56D ARG* 1.4 68.5 + - - +
58D SER* 3.6 5.5 + - - -
59D SER* 2.9 32.2 + - - -
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 4.4 10.7 - - - +
21D ASP* 4.1 16.4 + - - -
52D VAL* 3.1 41.9 + - - +
53D VAL* 3.0 8.1 + - - +
55D ALA* 1.4 88.2 - - - +
57D ARG* 1.3 55.0 + - - +
59D SER* 3.3 2.4 + - - -
60D TRP* 2.8 36.0 + - - +
89D ILE* 3.4 11.8 - - + +
92D GLU* 3.2 47.6 + - + +
93D LEU* 3.8 26.2 - - + +
96D VAL* 4.7 11.5 - - - +
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 4.1 13.3 - - - +
53D VAL* 2.9 26.6 + - + +
54D GLY* 3.5 14.0 - - - +
56D ARG* 1.3 75.1 - - - +
58D SER* 1.4 55.9 + - - +
60D TRP* 3.4 4.4 + - - +
61D ARG* 3.0 59.6 + - - +
93D LEU* 3.8 19.3 - - + -
132D ARG* 4.3 5.1 - - - +
133D TYR* 3.3 51.3 + - + +
136D GLU* 3.1 37.0 + - - +
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Residues in contact with SER 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 5.3 6.1 + - - -
54D GLY 2.9 17.1 + - - -
55D ALA* 3.8 6.3 - - - -
57D ARG* 1.4 76.1 - - - +
59D SER* 1.4 61.1 + - - +
61D ARG* 3.4 22.8 + - - +
62D VAL* 3.2 30.1 + - - +
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 2.7 40.8 + - - +
18B GLU 5.1 0.2 + - - -
19B ARG* 3.7 20.0 + - - +
55D ALA 2.9 19.7 + - - -
56D ARG* 3.3 6.0 + - - -
58D SER* 1.4 71.2 - - - +
60D TRP* 1.3 60.7 + - - +
62D VAL* 3.2 4.4 + - - +
63D ILE* 2.9 34.6 + - - +
89D ILE* 4.2 8.5 - - - -
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG 2.8 21.7 + - - +
57D ARG* 3.6 7.2 - - - +
59D SER* 1.3 72.6 - - - +
61D ARG* 1.4 69.5 + - + +
63D ILE* 3.4 5.0 + - - +
64D SER* 2.8 59.4 + - - -
86D ARG* 3.4 23.5 - - + +
89D ILE* 3.8 9.3 - - + +
90D GLU* 2.9 47.7 + - + +
93D LEU* 4.7 3.1 - - + -
136D GLU* 3.5 23.1 - - + -
137D VAL* 3.4 29.2 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLY 4.9 1.2 + - - -
57D ARG* 3.0 55.5 + - - +
58D SER* 3.6 27.4 - - - +
59D SER 3.3 0.2 - - - -
60D TRP* 1.4 91.9 - - + +
62D VAL* 1.3 56.1 - - + +
64D SER* 3.8 3.0 - - - -
65D SER* 3.0 30.7 + - - -
136D GLU* 4.6 4.9 + - - -
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.4 47.8 - - + +
17B ALA* 3.9 4.7 - - - +
18B GLU* 6.2 0.2 - - - +
58D SER* 3.2 21.0 + - - +
59D SER* 3.2 8.3 + - - +
61D ARG* 1.3 75.6 - - + +
63D ILE* 1.4 61.4 + - + +
65D SER* 3.4 8.3 + - - -
66D ILE* 3.1 30.0 + - + +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 25.8 - - + +
17B ALA* 3.6 22.2 - - + -
59D SER 2.9 20.1 + - - +
60D TRP* 3.9 3.4 - - - +
62D VAL* 1.4 70.4 - - - +
64D SER* 1.4 54.9 + - - +
66D ILE* 3.1 10.7 + - + +
67D GLU* 2.8 33.1 + - - +
82D VAL* 3.4 33.3 - - + +
85D TYR* 3.6 17.3 - - + -
86D ARG* 3.7 22.9 - - + +
89D ILE* 3.8 18.8 - - + -
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Residues in contact with SER 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 2.8 57.7 + - - -
61D ARG* 3.8 4.9 - - - -
63D ILE* 1.4 71.3 - - - +
65D SER* 1.4 57.5 + - - +
67D GLU* 3.3 13.7 + - - +
68D GLN* 3.0 34.4 + - - +
86D ARG* 3.4 12.0 - - - +
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG 3.0 19.3 + - - -
62D VAL* 3.4 8.7 - - - -
63D ILE 3.3 0.2 - - - -
64D SER* 1.4 73.9 - - - +
66D ILE* 1.4 62.7 + - - +
68D GLN* 3.5 8.0 + - - +
69D LYS* 3.3 28.1 + - - +
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.8 29.6 - - + -
16B GLN* 3.4 42.0 - - + +
62D VAL* 3.1 32.0 + - + +
63D ILE* 3.5 7.6 - - + +
65D SER* 1.4 72.6 - - - +
67D GLU* 1.4 55.3 + - - +
69D LYS* 3.2 7.7 + - - +
70D THR* 2.7 36.7 + - - -
78D LYS* 5.2 8.1 - - - +
82D VAL* 4.2 12.6 - - + -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 2.8 16.0 + - + +
64D SER* 3.4 12.8 - - - +
66D ILE* 1.4 73.1 - - - +
68D GLN* 1.4 58.9 + - - +
70D THR* 4.0 3.9 - - - -
71D SER* 3.0 32.7 + - - -
79D ILE* 5.1 5.4 - - + +
82D VAL* 3.7 18.4 - - + +
83D ARG* 3.3 38.5 + - + +
86D ARG* 2.8 41.0 + - + +
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Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D SER* 3.0 16.3 + - - +
65D SER* 3.7 11.0 - - - +
66D ILE 3.3 0.2 - - - -
67D GLU* 1.4 78.7 - - + +
69D LYS* 1.3 62.6 + - + +
71D SER* 3.7 11.1 + - - -
72D ALA* 3.7 11.3 + - - +
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D SER* 3.3 17.2 + - - +
66D ILE* 3.2 10.0 + - - +
68D GLN* 1.3 76.4 - - + +
70D THR* 1.4 62.0 + - - +
72D ALA* 3.4 19.7 + - - +
73D ASP* 3.5 9.8 + - - +
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ILE* 2.7 26.9 + - - -
67D GLU* 4.0 6.1 - - - -
69D LYS* 1.4 70.1 - - - +
71D SER* 1.4 63.9 + - - +
73D ASP* 3.1 29.7 - - - +
74D GLY 3.5 4.3 + - - -
75D ASN* 4.1 1.2 + - - +
78D LYS* 4.7 24.5 - - - -
79D ILE* 3.7 18.0 - - - +
82D VAL* 4.9 7.4 - - - -
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 3.0 20.9 + - - -
68D GLN* 3.8 8.3 - - - -
69D LYS 3.3 0.4 - - - -
70D THR* 1.4 76.3 - - - +
72D ALA* 1.4 61.2 + - - +
74D GLY* 3.6 10.9 + - - -
79D ILE* 4.0 13.9 - - - +
83D ARG* 5.3 9.9 - - - -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLN 3.7 8.3 + - - +
69D LYS* 3.4 13.4 + - - +
70D THR 3.3 0.4 - - - -
71D SER* 1.4 78.5 - - - +
73D ASP* 1.4 62.2 + - - +
74D GLY 3.6 0.5 + - - -
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Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LYS 3.5 6.2 + - - +
70D THR* 3.1 33.5 - - - +
72D ALA* 1.4 78.9 - - - +
74D GLY* 1.3 61.4 + - - +
75D ASN* 3.3 22.2 + - - +
78D LYS* 5.4 5.7 + - - +
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Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR 3.5 4.2 + - - -
71D SER* 3.6 10.0 + - - -
72D ALA 3.3 3.8 - - - -
73D ASP* 1.3 81.0 + - - +
75D ASN* 1.3 59.7 + - - +
76D GLU 3.8 3.2 + - - -
79D ILE* 5.8 0.9 - - - -
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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