Contacts of the helix formed by residues 38 - 74 (chain A) in PDB entry 4E2E
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO 4.2 0.2 + - - -
37A LEU* 1.3 76.5 - - - +
39A ASN* 1.3 66.4 + - - +
40A GLU* 3.8 9.4 + - - +
41A GLU* 3.0 38.0 + - - +
42A ARG* 3.0 23.3 + - - +
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 1.3 72.4 - - - +
40A GLU* 1.3 56.2 + - - +
42A ARG* 2.7 37.6 + - - +
43A ASN* 3.0 37.7 + - - +
118A GLU* 4.7 14.8 + - - +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.4 3.0 - - - +
12A ARG* 2.4 48.6 + - - -
38A SER* 3.8 9.4 - - - +
39A ASN* 1.3 76.2 - - - +
41A GLU* 1.3 60.3 + - + +
43A ASN* 3.4 4.8 + - - +
44A LEU* 3.1 54.6 + - - +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 2.9 46.8 + - - -
8A VAL* 3.6 32.3 - - + +
27A MSE 3.2 23.4 - - + +
30A VAL* 4.2 3.8 - - - -
36A PRO 4.1 0.2 - - - +
37A LEU* 3.5 10.3 - - + -
38A SER* 3.0 36.6 + - - +
40A GLU* 1.3 75.1 - - + +
42A ARG* 1.3 57.6 + - - +
44A LEU* 3.4 4.1 + - - -
45A LEU* 3.0 26.5 + - - +
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 5.9 1.0 - - - +
37A LEU* 2.9 37.6 + - + +
38A SER* 3.0 8.5 + - - +
39A ASN* 2.7 46.9 + - - +
41A GLU* 1.3 72.5 - - - +
43A ASN* 1.4 59.8 + - - +
45A LEU* 3.5 4.9 + - - +
46A SER* 3.1 26.3 + - - -
116A GLN* 6.2 0.2 - - - +
118A GLU 5.9 0.2 - - - -
119A SER* 2.7 32.4 + - - +
122A PHE* 3.5 41.9 - - + -
123A TYR* 3.2 45.7 + - + +
171A ILE* 6.5 0.2 - - - -
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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 ASN* 3.0 24.4 + - - +
40A GLU* 3.4 5.6 + - - +
42A ARG* 1.4 76.2 - - - +
44A LEU* 1.4 56.6 + - - +
46A SER* 3.2 6.4 + - - -
47A VAL* 2.8 44.3 + - + +
122A PHE* 3.7 24.5 - - - -
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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
----------------------------------------------------------
8A VAL* 3.6 32.5 - - + +
11A ALA* 4.7 1.1 - - + -
12A ARG* 4.1 22.4 - - + +
15A GLU* 4.1 8.5 - - - +
23A MSE 3.4 27.6 - - + +
27A MSE 3.8 21.9 - - + +
40A GLU* 3.1 40.8 + - - +
41A GLU* 3.6 8.3 - - - +
43A ASN* 1.4 75.0 - - - +
45A LEU* 1.3 55.8 + - - +
47A VAL* 4.7 1.1 - - - -
48A ALA* 3.0 30.5 + - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MSE 3.8 27.5 - - + +
31A THR* 4.1 12.8 - - - +
37A LEU* 3.9 15.5 - - + -
41A GLU 3.0 17.9 + - - +
42A ARG* 3.6 5.2 - - - +
43A ASN 3.3 0.2 - - - -
44A LEU* 1.3 74.6 - - - +
46A SER* 1.3 61.3 + - - +
48A ALA* 3.4 1.1 + - - +
49A TYR* 3.2 58.2 + - + +
100A VAL* 5.7 1.3 - - + -
103A LEU* 4.2 8.1 - - + -
108A LEU* 3.6 31.4 - - + -
123A TYR* 5.2 2.2 - - + -
126A MSE 4.6 17.9 - - + +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG 3.1 14.8 + - - -
43A ASN* 3.2 11.4 + - - -
45A LEU* 1.3 73.5 - - - +
47A VAL* 1.3 59.1 + - - +
49A TYR* 3.6 0.5 + - - -
50A LYS* 3.0 32.7 + - - +
122A PHE* 3.8 21.2 - - - -
125A LYS* 5.4 5.4 + - - -
126A MSE 4.3 22.3 - - - +
130A TYR* 4.3 2.9 + - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.7 24.5 - - + +
20A TYR* 4.9 1.6 - - + -
23A MSE 3.9 13.0 - - + -
43A ASN* 2.8 30.1 + - + +
44A LEU* 4.0 3.6 - - - +
46A SER* 1.3 72.1 - - - +
48A ALA* 1.4 63.1 + - - +
50A LYS* 3.8 5.5 - - - +
51A ASN* 2.8 45.2 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.3 2.2 - - - +
23A MSE 3.8 24.0 - - + +
24A ALA* 3.5 32.8 - - - +
27A MSE 4.8 0.4 - - + -
44A LEU 3.0 19.5 + - - +
45A LEU* 3.6 7.4 - - - +
46A SER 3.3 0.2 - - - -
47A VAL* 1.4 78.5 - - - +
49A TYR* 1.3 57.8 + - + +
51A ASN* 3.2 3.1 + - - +
52A VAL* 3.1 32.0 + - - +
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.7 32.4 + - + -
25A ALA* 5.3 0.2 - - - -
28A LYS* 3.5 22.9 - - - +
45A LEU* 3.2 46.9 + - + +
46A SER 4.4 0.9 - - - +
48A ALA* 1.3 75.9 - - - +
50A LYS* 1.3 58.3 + - - +
52A VAL* 3.9 5.1 - - + +
53A VAL* 2.9 33.4 + - - +
96A VAL* 4.0 17.5 - - + -
99A ASP* 2.9 30.0 + - - -
100A VAL* 3.3 33.7 - - + -
103A LEU* 4.0 11.3 - - + +
126A MSE 5.1 1.6 - - + -
130A TYR* 3.2 15.9 - - + +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.0 21.8 + - - +
47A VAL* 3.8 7.6 - - - +
48A ALA 3.3 0.2 - - - -
49A TYR* 1.3 74.8 - - - +
51A ASN* 1.3 61.9 + - - +
53A VAL* 3.7 5.0 - - + +
54A GLY* 2.9 26.5 + - - -
57A ARG* 5.4 7.5 - - - +
130A TYR* 3.3 8.4 + - - +
133A TYR* 4.7 17.5 + - - +
178A ASN* 6.2 2.2 - - - +
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.4 53.3 + - + +
47A VAL* 2.8 40.8 + - - +
48A ALA 3.7 0.7 - - - +
50A LYS* 1.3 78.7 - - - +
52A VAL* 1.3 64.3 + - - +
54A GLY* 4.0 1.5 - - - -
55A ALA* 3.2 22.7 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.4 32.1 - - + +
21A ASP* 3.5 26.9 - - - +
24A ALA* 4.0 9.0 - - + -
48A ALA 3.1 16.1 + - - +
49A TYR* 3.3 10.3 + - + +
51A ASN* 1.3 73.8 - - - +
53A VAL* 1.3 62.8 + - - +
55A ALA* 3.4 2.7 + - - -
56A ARG* 3.3 38.9 + - - +
96A VAL* 3.8 31.2 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR 2.9 19.7 + - - +
50A LYS* 3.7 7.9 - - + +
52A VAL* 1.3 73.3 - - - +
54A GLY* 1.3 58.2 + - - +
56A ARG* 3.2 5.8 + - + +
57A ARG* 2.8 52.8 + - + +
93A LEU* 4.4 9.6 - - + +
96A VAL* 4.0 13.0 - - + -
97A CYS* 3.9 28.0 - - - -
130A TYR* 3.8 11.7 - - + +
133A TYR* 3.7 34.8 - - + -
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS 2.9 21.1 + - - -
51A ASN* 4.0 1.8 - - - -
52A VAL 3.3 0.2 - - - -
53A VAL* 1.3 79.5 - - - +
55A ALA* 1.3 54.8 + - - +
57A ARG* 3.5 14.7 + - - +
58A SER* 3.0 30.1 + - - -
61A ARG* 4.8 2.0 + - - -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN 3.2 17.9 + - - +
52A VAL* 3.7 5.6 - - - +
53A VAL 3.3 0.2 - - - -
54A GLY* 1.3 73.7 - - - +
56A ARG* 1.3 70.3 + - - +
58A SER* 3.5 6.1 + - - -
59A SER* 3.0 32.9 + - - -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 3.3 35.0 + - - -
52A VAL* 3.4 30.4 + - - +
53A VAL* 3.2 8.4 + - - +
55A ALA* 1.3 89.8 - - - +
57A ARG* 1.3 59.1 + - - +
59A SER* 3.4 4.0 + - - -
60A TRP* 2.9 30.5 + - - +
89A ILE* 3.5 10.8 - - + +
92A GLU* 3.2 37.7 + - - +
93A LEU* 3.9 32.0 - - + +
96A VAL* 4.4 12.1 - - + +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 5.4 7.5 - - - +
53A VAL* 2.8 36.4 + - + +
54A GLY* 3.8 9.9 - - - +
56A ARG* 1.3 70.5 - - - +
58A SER* 1.3 58.2 + - - +
60A TRP* 3.5 3.5 + - - +
61A ARG* 3.0 65.8 + - - +
93A LEU* 3.8 22.2 - - + -
132A ARG* 4.4 6.1 - - - +
133A TYR* 3.5 42.3 + - + -
136A GLU* 2.8 41.1 + - - +
185A GLU* 5.3 2.2 + - - -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.0 17.8 + - - -
55A ALA* 3.7 7.2 - - - -
56A ARG 3.3 0.2 - - - -
57A ARG* 1.3 76.9 - - - +
59A SER* 1.4 62.0 + - - +
61A ARG* 3.4 23.1 + - - +
62A VAL* 3.1 33.9 + - - +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 3.0 19.3 + - - +
56A ARG* 3.8 5.6 - - - -
57A ARG 3.4 0.2 - - - -
58A SER* 1.4 71.9 + - - +
60A TRP* 1.3 66.1 + - - +
62A VAL* 3.3 7.7 + - - +
63A ILE* 3.1 28.9 + - - +
89A ILE* 4.0 24.2 - - - -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG 2.9 17.5 + - - +
57A ARG* 3.8 4.7 - - - +
59A SER* 1.3 75.0 - - - +
61A ARG* 1.3 72.3 + - + +
63A ILE* 3.9 2.1 - - - +
64A SER* 2.7 56.1 + - - -
86A ARG* 3.5 16.9 - - + +
89A ILE* 3.6 11.5 - - + +
90A GLU* 2.8 53.4 + - + +
93A LEU* 4.3 7.0 - - + -
136A GLU* 3.7 23.6 - - + -
137A VAL* 3.5 31.9 - - + -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY* 4.8 2.4 + - - -
57A ARG* 3.0 63.9 + - - +
58A SER* 3.6 27.4 + - - +
60A TRP* 1.3 93.4 - - + +
62A VAL* 1.3 56.7 + - + +
64A SER* 3.9 2.6 - - - -
65A SER* 3.0 30.5 + - - -
136A GLU* 5.6 2.8 + - - -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 3.1 23.6 + - - +
59A SER* 3.3 10.1 + - - +
61A ARG* 1.3 76.7 - - + +
63A ILE* 1.3 68.5 + - + +
65A SER* 3.4 7.3 + - - -
66A ILE* 3.2 39.3 + - + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.1 17.7 + - - +
60A TRP* 4.2 2.5 - - - +
62A VAL* 1.3 80.8 - - + +
64A SER* 1.3 60.2 + - - +
66A ILE* 3.3 20.0 + - + +
67A GLU* 2.8 27.3 + - - +
82A VAL* 3.7 15.2 - - + +
85A TYR* 3.9 22.9 - - + -
86A ARG* 3.6 36.1 - - + +
89A ILE* 3.6 21.3 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 2.7 55.7 + - - -
61A ARG* 3.9 4.0 - - - -
63A ILE* 1.3 71.4 - - - +
65A SER* 1.3 63.2 + - - +
67A GLU* 3.3 15.2 + - - +
68A GLN* 3.1 39.8 + - - +
86A ARG* 3.4 11.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG 3.0 19.3 + - - -
62A VAL* 3.5 8.5 - - - -
63A ILE 3.3 0.2 - - - -
64A SER* 1.3 76.7 - - - +
66A ILE* 1.4 61.2 + - - +
68A GLN* 3.4 12.8 + - - +
69A LYS* 3.1 49.0 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.2 32.0 + - + +
63A ILE* 3.3 20.1 + - + +
65A SER* 1.4 74.5 - - - +
67A GLU* 1.4 51.3 + - - +
69A LYS* 3.1 11.3 + - + +
70A THR* 2.8 48.9 + - - +
82A VAL* 3.9 16.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE 2.8 12.8 + - - +
64A SER* 3.3 13.4 + - - +
66A ILE* 1.4 76.2 - - - +
68A GLN* 1.3 59.4 + - + +
70A THR* 3.5 2.5 + - - -
71A SER* 3.1 35.5 + - - +
79A ILE* 5.6 3.8 - - + +
82A VAL* 3.6 19.4 - - + +
83A ARG* 3.6 25.1 - - + +
86A ARG* 2.7 53.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.1 32.3 + - - +
65A SER* 3.7 10.7 - - - +
66A ILE 3.4 0.2 - - - -
67A GLU* 1.3 76.8 - - + +
69A LYS* 1.3 63.6 + - + +
71A SER* 3.9 5.4 + - - -
72A ALA* 3.4 21.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER* 3.1 34.6 + - - +
66A ILE* 3.1 12.4 + - + +
68A GLN* 1.3 78.6 - - + +
70A THR* 1.4 52.9 + - - +
72A ALA* 3.3 7.8 + - - +
73A ASP* 2.8 33.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 2.8 30.4 + - - +
67A GLU* 3.5 4.5 + - - -
69A LYS* 1.4 72.7 - - - +
71A SER* 1.4 63.6 + - - +
73A ASP* 3.3 20.3 + - + +
74A GLY 3.5 5.5 + - - -
75A ASN* 4.0 5.1 + - + +
78A LYS* 3.8 21.3 - - + -
79A ILE* 3.8 38.6 - - + +
82A VAL* 4.0 12.1 - - + +
----------------------------------------------------------
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.1 22.9 + - - +
68A GLN* 4.1 6.1 - - - -
69A LYS 3.4 0.2 - - - -
70A THR* 1.4 74.8 - - - +
72A ALA* 1.4 60.0 + - - +
74A GLY* 3.6 11.3 + - - -
79A ILE* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 3.4 16.4 + - - +
69A LYS* 3.3 8.9 + - - +
71A SER* 1.4 76.9 - - - +
73A ASP* 1.4 60.2 + - - +
74A GLY* 3.3 2.1 + - - -
----------------------------------------------------------
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS 2.8 16.9 + - - +
70A THR* 3.3 14.5 + - + +
72A ALA* 1.4 75.1 - - - +
74A GLY* 1.3 58.2 + - - +
75A ASN* 3.3 12.3 + - + +
----------------------------------------------------------
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR 3.5 4.4 + - - -
71A SER 3.6 8.2 + - - -
72A ALA 3.3 4.7 - - - -
73A ASP* 1.3 76.9 - - - +
75A ASN* 1.4 57.8 + - - +
76A GLU* 3.1 10.7 + - - +
79A ILE* 5.1 2.9 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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