Contacts of the helix formed by residues 34 - 62 (chain A) in PDB entry 5WIU
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 GLY 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 1.3 66.4 + - - +
36A ALA* 3.2 6.7 - - - +
37A ALA* 3.3 9.8 + - - +
38A LEU* 3.1 22.7 + - - +
95A GLU 4.8 2.9 - - - -
96A VAL* 3.7 33.2 - - - +
1206A OLA 4.8 9.9 + - - -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY* 1.3 75.5 - - - +
36A ALA* 1.3 57.0 + - - +
38A LEU* 3.3 8.8 + - - +
39A VAL* 2.8 40.2 + - + +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.2 4.6 - - - +
35A ALA* 1.3 76.2 - - - +
37A ALA* 1.3 60.5 + - - +
39A VAL* 4.2 4.9 - - - +
40A GLY* 2.9 28.1 + - - -
1206A OLA 3.8 23.4 - - + +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY* 3.3 11.8 + - - +
36A ALA* 1.3 78.7 - - - +
38A LEU* 1.3 59.1 + - - +
41A GLY* 2.8 28.4 + - - -
92A VAL* 3.7 5.4 - - - +
95A GLU* 3.8 40.8 - - + +
96A VAL* 4.1 2.9 - - + +
435A TRP* 3.7 7.8 - - + -
1206A OLA 3.9 24.7 - - + +
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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
----------------------------------------------------------
34A GLY 3.1 12.5 + - - +
35A ALA* 3.5 12.1 - - - +
37A ALA* 1.3 75.0 - - - +
39A VAL* 1.3 63.8 + - + +
42A VAL* 2.9 53.5 + - + +
92A VAL* 4.3 10.0 - - + +
96A VAL* 3.9 19.2 - - + +
1217A PEG 4.7 8.7 - - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 2.8 28.0 + - + +
36A ALA* 4.2 4.3 - - - +
38A LEU* 1.3 75.9 - - + +
40A GLY* 1.3 65.2 + - - +
42A VAL* 3.9 4.3 - - - +
43A LEU* 3.0 41.2 + - + +
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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
----------------------------------------------------------
36A ALA 2.9 17.1 + - - -
39A VAL* 1.3 78.9 - - - +
41A GLY* 1.3 56.7 + - - +
43A LEU* 3.5 8.0 + - - +
44A LEU* 2.8 30.1 + - - +
435A TRP* 4.3 6.1 - - - -
1206A OLA 3.9 26.5 - - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 2.8 24.2 + - - -
38A LEU 3.8 0.4 - - - -
40A GLY* 1.3 70.9 - - - +
42A VAL* 1.3 59.1 + - - +
44A LEU* 3.2 3.1 + - - +
45A ILE* 2.9 35.3 + - - +
92A VAL* 3.6 25.1 - - - +
435A TRP* 3.8 10.4 - - - -
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Residues in contact with VAL 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 39.4 + - + +
39A VAL* 3.9 4.5 - - - +
41A GLY* 1.3 74.7 - - - +
43A LEU* 1.3 68.6 + - + +
45A ILE* 3.9 1.4 - - - +
46A GLY* 2.9 21.8 + - - -
1217A PEG 3.9 38.5 + - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.0 36.9 + - + +
40A GLY* 3.7 6.3 - - - +
42A VAL* 1.3 81.6 - - + +
44A LEU* 1.3 57.0 + - - +
46A GLY* 3.7 1.2 - - - -
47A ALA* 2.9 31.2 + - - +
1206A OLA 3.8 22.1 - - + +
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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
----------------------------------------------------------
40A GLY 2.8 19.8 + - - +
41A GLY* 3.2 6.0 + - - +
43A LEU* 1.3 75.0 - - - +
45A ILE* 1.3 58.1 + - + +
47A ALA* 3.2 1.7 + - - +
48A VAL* 2.9 45.1 + - + +
88A LEU* 4.2 19.1 - - + -
91A PHE* 5.7 0.7 - - + -
92A VAL* 6.1 1.6 - - + -
435A TRP* 4.1 23.1 - - + -
438A TYR* 4.0 27.4 - - + +
439A VAL* 3.9 27.1 - - + +
442A ALA* 4.2 7.9 - - + -
1206A OLA 3.6 23.3 - - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 2.9 21.4 + - - +
42A VAL 3.9 3.1 - - - +
44A LEU* 1.3 75.2 - - + +
46A GLY* 1.3 63.7 + - - +
48A VAL* 3.4 2.6 + - - +
49A LEU* 3.0 44.4 + - + +
84A ALA* 4.0 11.9 - - + +
88A LEU* 3.6 32.1 - - + +
89A PRO* 3.8 30.1 - - + -
92A VAL* 4.1 8.1 - - + -
1217A PEG 3.8 40.8 - - - +
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Residues in contact with GLY 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 VAL 2.9 15.3 + - - -
43A LEU* 3.7 2.7 - - - -
45A ILE* 1.3 78.7 - - - +
47A ALA* 1.3 55.7 + - - +
49A LEU* 3.9 5.8 - - - +
50A ALA* 2.9 32.8 + - - +
1217A PEG 4.8 3.3 + - - -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 2.9 18.3 + - - +
44A LEU 3.2 2.9 + - - +
46A GLY* 1.3 75.3 - - - +
48A VAL* 1.3 62.8 + - - +
50A ALA* 4.8 2.9 - - - -
51A GLY* 3.0 22.9 + - - -
52A ASN* 5.0 0.2 + - - -
442A ALA* 4.2 17.6 - - + +
1206A OLA 3.6 23.8 - - + -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.9 32.4 + - + +
45A ILE 3.8 3.6 - - - +
47A ALA* 1.3 76.3 - - - +
49A LEU* 1.3 64.5 - - - +
52A ASN* 2.8 45.7 + - - +
80A ASP* 3.3 30.5 - - + +
81A LEU 4.5 0.4 - - - +
84A ALA* 3.7 11.4 - - + -
88A LEU* 4.5 8.1 - - + -
441A SER* 3.8 14.6 - - - +
442A ALA* 3.8 25.6 - - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.0 37.5 + - + +
46A GLY* 3.9 5.4 - - - +
48A VAL* 1.3 78.4 - - - +
50A ALA* 1.3 62.8 + - - +
53A SER* 2.8 31.7 + - - +
81A LEU* 3.6 17.8 - - + +
84A ALA* 3.6 22.0 - - + +
85A LEU* 3.7 31.4 - - + -
1217A PEG 5.5 2.9 - - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 2.9 18.3 + - - +
47A ALA* 4.3 2.9 - - - +
49A LEU* 1.3 78.4 - - - +
51A GLY* 1.3 62.6 + - - +
53A SER* 4.0 3.2 - - - -
54A LEU* 3.1 37.5 + - + +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.0 17.5 + - - -
50A ALA* 1.3 76.7 - - - +
52A ASN* 1.3 61.3 + - - +
54A LEU* 3.3 5.0 + - - +
55A VAL* 3.2 19.9 + - - +
442A ALA 5.9 0.2 - - - -
445A PRO* 3.3 29.3 - - - +
1209A OLA 3.9 15.9 - - - +
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Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.8 33.8 + - - +
51A GLY* 1.3 73.6 - - - +
53A SER* 1.3 65.9 + - - +
55A VAL* 3.4 6.2 + - - +
56A CYS* 3.1 27.0 + - - -
77A ALA* 3.5 22.1 - - + +
80A ASP* 3.7 16.9 - - - +
81A LEU* 3.7 20.9 - - + -
441A SER 2.9 25.7 + - - -
442A ALA* 4.9 0.2 - - - +
444A ASN* 5.1 2.6 - - - +
445A PRO* 3.8 17.2 - - - +
448A TYR* 5.9 1.4 - - - -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 2.8 24.7 + - - +
50A ALA* 4.0 4.5 - - - -
52A ASN* 1.3 75.6 - - - +
54A LEU* 1.3 58.2 - - - +
56A CYS* 3.1 6.3 + - - +
57A VAL* 2.9 39.3 + - - +
81A LEU* 3.6 17.0 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.1 31.8 + - + +
51A GLY 3.6 1.6 - - - +
52A ASN 3.2 0.2 - - - -
53A SER* 1.3 77.3 - - - +
55A VAL* 1.3 54.6 + - - +
57A VAL* 4.3 5.4 - - + +
58A SER* 2.7 38.2 + - - +
1209A OLA 3.5 42.7 - - + +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 3.2 14.5 + - - +
52A ASN* 3.6 9.9 - - - +
53A SER 3.2 0.2 - - - -
54A LEU* 1.3 75.5 - - - +
56A CYS* 1.3 66.6 + - - +
58A SER* 3.2 3.1 + - - -
59A VAL* 3.1 28.0 + - + +
73A ILE* 4.1 26.7 - - + +
74A VAL* 5.2 0.9 - - - -
77A ALA* 4.1 15.5 - - + -
445A PRO* 3.9 11.0 - - + -
448A TYR* 3.8 24.9 - - + -
455A PHE* 4.4 9.0 - - + -
1209A OLA 3.8 21.8 - - + -
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Residues in contact with CYS 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 ASN 3.1 17.9 + - - +
53A SER* 3.1 8.7 + - - +
55A VAL* 1.3 78.3 - - - +
57A VAL* 1.3 64.4 + - + +
59A VAL* 3.5 3.6 + - - +
60A ALA* 3.1 20.6 + - - +
74A VAL* 4.3 27.3 - - + +
77A ALA* 3.7 20.6 - - - -
78A ALA* 4.7 3.8 - - - -
81A LEU* 4.2 16.2 - - + -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 2.9 25.2 + - - +
54A LEU* 4.3 5.4 - - + +
56A CYS* 1.3 76.3 - - + +
58A SER* 1.3 55.8 + - - +
60A ALA* 3.1 8.7 + - + +
61A THR* 2.7 48.3 + - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.7 25.8 + - - +
55A VAL 3.2 4.9 + - - -
57A VAL* 1.3 75.2 - - - +
59A VAL* 1.3 64.4 + - - +
61A THR* 3.3 8.8 + - - -
62A GLU* 3.0 29.1 + - - +
65A LEU* 3.6 18.0 - - - +
455A PHE* 4.6 1.3 - - - -
458A VAL* 4.1 6.5 - - - +
1209A OLA 3.2 29.1 - - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.1 18.7 + - + +
56A CYS 3.9 1.8 - - - +
58A SER* 1.3 76.9 - - - +
60A ALA* 1.3 61.4 + - - +
62A GLU 3.7 2.6 - - - +
65A LEU* 3.8 22.7 - - + +
66A GLN* 3.2 21.6 + - + +
70A ASN* 4.5 6.3 - - + +
73A ILE* 5.5 0.7 - - + -
74A VAL* 3.7 23.3 - - + -
455A PHE* 4.0 24.7 - - + -
1205A OLA 3.4 41.7 - - + +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS 3.1 13.0 + - - +
57A VAL* 3.1 14.8 + - + +
59A VAL* 1.3 79.9 - - - +
61A THR* 1.3 63.4 + - + +
66A GLN* 3.5 14.6 + - - +
1218A PEG 4.8 21.1 - - - +
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.7 38.7 + - + +
58A SER* 3.3 10.4 + - - -
60A ALA* 1.3 76.4 - - + +
62A GLU* 1.3 64.3 + - - +
63A ARG 4.0 1.4 + - - -
66A GLN* 4.9 0.7 - - - -
458A VAL* 5.5 2.6 - - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 3.0 16.2 + - - +
59A VAL 3.7 3.1 - - - +
60A ALA 3.5 1.0 - - - -
61A THR* 1.3 80.6 - - - +
63A ARG* 1.3 65.4 + - - +
64A ALA* 4.4 5.2 - - + +
65A LEU* 3.2 26.6 + - + +
66A GLN* 3.6 17.0 + - - +
458A VAL* 4.3 16.6 - - + -
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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