Contacts of the helix formed by residues 13 - 39 (chain J) in PDB entry 6WC2
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 13 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 3.5 4.0 - - + +
12J MET* 1.3 74.7 - - - +
14J GLU* 1.3 53.4 + - - +
15J ARG* 3.4 16.1 + - - +
16J ASN* 2.8 52.2 + - + +
17J ARG* 2.8 34.6 + - - +
194N LYS 4.2 16.0 - - - +
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Residues in contact with GLU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J MET 3.4 6.0 + - - +
13J ASP* 1.3 71.1 + - - +
15J ARG* 1.3 65.6 + - + +
17J ARG* 3.4 25.4 + - - +
18J GLN* 3.0 26.2 + - + +
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Residues in contact with ARG 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E A 4.2 19.8 + - - -
6E C 3.7 33.1 + - - +
7E T 6.5 0.2 - - + -
13J ASP* 3.3 14.2 + - - +
14J GLU* 1.3 80.3 - - + +
16J ASN* 1.3 64.6 + - - +
18J GLN* 3.3 8.5 + - - +
19J VAL* 3.1 27.1 + - + +
191N TYR* 3.1 58.7 + - + +
194N LYS* 3.8 33.6 - - - +
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Residues in contact with ASN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 4.0 13.4 - - + +
13J ASP* 2.8 37.2 + - - +
15J ARG* 1.3 70.6 - - - +
17J ARG* 1.3 66.1 + - - +
19J VAL* 3.3 9.6 + - - +
20J THR* 3.0 28.3 + - - +
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Residues in contact with ARG 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I LEU 4.1 5.1 + - - +
39I CYS* 3.5 46.3 + - + +
40I ASP* 4.5 2.6 + - - +
10J ARG* 3.8 21.0 - - - +
11J ILE* 3.0 37.7 + - + +
12J MET* 4.3 11.4 + - - +
13J ASP 2.8 18.6 + - - +
14J GLU* 3.6 28.9 - - - +
15J ARG 3.3 0.2 - - - -
16J ASN* 1.3 78.3 - - - +
18J GLN* 1.3 56.5 + - - +
20J THR* 3.4 0.3 + - - -
21J PHE* 2.9 28.3 + - + +
50J SER* 3.6 24.5 + - - -
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Residues in contact with GLN 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E T 4.3 18.9 + - - +
14J GLU* 3.0 17.0 + - + +
15J ARG* 3.6 6.7 - - - +
17J ARG* 1.3 74.7 - - - +
19J VAL* 1.3 66.3 + - + +
21J PHE* 3.6 19.1 - - - +
22J THR* 3.0 55.1 + - - -
49J ASN* 4.6 10.9 + - - -
55J PHE* 6.2 1.0 - - - -
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Residues in contact with VAL 19 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E T 4.2 25.6 - - + -
8E T 4.4 18.2 - - + +
12F G 6.1 2.2 - - - +
13F A 5.8 2.5 - - - +
15J ARG* 3.1 16.6 + - + +
16J ASN* 3.3 11.6 + - - +
18J GLN* 1.3 76.3 - - + +
20J THR* 1.3 65.6 + - - +
22J THR* 3.4 4.7 + - - -
23J LYS* 3.2 46.4 + - + +
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Residues in contact with THR 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F A 3.4 27.3 + - - +
38I LEU* 4.4 5.2 - - + -
39I CYS* 3.9 8.5 - - - -
6J ILE* 5.6 0.7 - - + -
11J ILE* 3.8 24.9 - - + +
16J ASN* 3.0 17.1 + - - +
17J ARG 3.8 3.6 - - - -
19J VAL* 1.3 80.0 - - - +
21J PHE* 1.3 54.3 + - - +
23J LYS* 3.3 5.6 + - - +
24J ARG* 2.8 51.7 + - - +
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Residues in contact with PHE 21 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 4.0 11.2 - - + +
39I CYS* 3.6 15.0 - - + -
41I CYS* 3.4 33.9 - - - -
17J ARG* 2.9 19.6 + - + +
18J GLN* 3.6 25.1 - - - +
19J VAL 3.3 0.2 - - - -
20J THR* 1.3 76.3 - - - +
22J THR* 1.3 60.5 + - - +
25J LYS* 2.8 71.6 + - + +
47J ILE* 3.9 11.7 - - + -
49J ASN* 3.8 13.7 - - + -
55J PHE* 3.7 35.2 - + - -
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Residues in contact with THR 22 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E T 4.6 15.0 - - - +
18J GLN* 3.0 35.2 + - - -
19J VAL* 3.8 6.3 - - - -
20J THR 3.3 0.2 - - - -
21J PHE* 1.3 82.4 - - - +
23J LYS* 1.3 63.5 + - + +
25J LYS* 4.0 14.0 + - - +
26J PHE* 3.3 20.3 + - - +
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Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E T 4.6 4.9 - - + -
9E T 2.8 44.4 + - + -
10E C 4.0 3.6 - - - +
10F A 3.9 32.3 + - + -
11F A 3.9 13.2 + - + +
12F G 2.8 23.6 + - - -
13F A 4.1 2.6 - - - +
19J VAL* 3.2 33.7 + - + +
20J THR* 3.8 5.4 - - - +
22J THR* 1.3 80.1 - - + +
24J ARG* 1.3 65.1 + - + +
26J PHE* 3.4 4.2 + - - +
27J GLY 3.1 16.5 + - - -
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Residues in contact with ARG 24 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E A 6.3 0.8 - - - -
10F A 3.8 44.5 + - - +
11F A 2.6 31.9 + - - -
31I LYS* 4.7 8.5 + - - +
34I GLU* 3.0 41.4 + - - +
35I LEU* 3.8 25.2 - - + +
38I LEU* 3.6 23.2 - - - +
6J ILE* 4.1 7.5 - - - +
8J ILE* 5.0 2.0 - - - +
20J THR* 2.8 34.4 + - + +
23J LYS* 1.3 73.2 - - - +
25J LYS* 1.3 59.8 + - - +
27J GLY* 3.7 1.2 - - - +
28J LEU* 2.9 30.0 + - - +
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Residues in contact with LYS 25 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 4.0 16.3 - - + +
77I GLU* 2.9 27.5 + - - -
79I ARG* 5.4 0.2 - - - +
21J PHE* 2.8 56.9 + - + +
22J THR* 4.0 14.6 + - - +
24J ARG* 1.3 71.7 - - - +
26J PHE* 1.3 66.2 + - - +
28J LEU* 3.3 3.9 + - - +
29J MET* 3.0 40.6 + - + +
47J ILE* 4.0 9.6 - - + -
55J PHE* 3.5 32.3 - - + -
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Residues in contact with PHE 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ARG* 5.9 7.0 - - - -
84I ILE* 4.2 30.1 - - + -
87I THR* 3.7 34.5 - - + -
88I LEU* 4.0 24.0 - - + -
91I ARG* 3.8 35.7 - - - +
22J THR 3.3 11.0 + - - +
23J LYS* 3.9 8.1 - - - +
24J ARG 3.3 0.4 - - - -
25J LYS* 1.3 83.7 - - - +
27J GLY* 1.3 54.0 + - - +
29J MET* 3.2 11.2 + - + +
30J LYS* 2.8 42.4 + - + +
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Residues in contact with GLY 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F T 5.1 6.3 + - - +
10F A 3.4 27.1 - - - -
31I LYS* 5.2 4.0 - - - +
23J LYS 3.1 11.1 + - - -
24J ARG 3.3 1.7 + - - -
26J PHE* 1.3 78.4 - - - +
28J LEU* 1.3 55.9 + - - +
30J LYS* 3.4 9.2 + - - +
31J LYS* 3.1 32.9 + - - +
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Residues in contact with LEU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F A 5.3 0.2 + - - -
28I LEU* 3.5 44.0 - - + +
31I LYS* 3.7 15.4 - - + +
32I ALA* 3.6 24.9 - - + +
35I LEU* 4.0 22.7 - - + -
43I ILE* 4.5 2.5 - - + -
45I LEU* 6.3 0.2 - - + -
24J ARG 2.9 17.6 + - - +
25J LYS 3.5 4.7 - - - +
27J GLY* 1.3 74.1 - - - +
29J MET* 1.3 59.7 + - - +
31J LYS* 3.3 4.0 + - + -
32J ALA* 3.0 24.8 + - - +
45J LEU* 3.9 32.3 - - + -
47J ILE* 4.2 7.0 - - + -
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Residues in contact with MET 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLU* 4.4 5.4 - - - +
79I ARG* 3.8 26.9 - - + -
84I ILE* 3.9 19.4 - - + +
25J LYS* 3.0 46.4 + - + +
26J PHE* 3.7 10.8 - - + +
28J LEU* 1.3 71.7 - - - +
30J LYS* 1.3 61.2 + - - +
32J ALA* 3.2 8.3 + - - +
33J TYR* 2.9 30.0 + - - +
45J LEU* 4.1 9.6 - - + -
47J ILE* 4.4 10.5 - - + -
55J PHE* 4.5 5.2 - - + -
56J GLN 3.8 24.7 - - - +
57J TYR* 3.9 21.0 - - + +
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Residues in contact with LYS 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F T 4.3 2.8 + - - -
9F T 2.6 40.2 + - - +
84I ILE* 4.4 10.3 - - + +
88I LEU* 3.7 41.5 - - + +
26J PHE* 2.8 32.4 + - + +
27J GLY* 3.6 8.5 - - - +
28J LEU 3.2 0.2 - - - -
29J MET* 1.3 76.3 - - - +
31J LYS* 1.3 57.4 + - - +
33J TYR* 3.3 4.3 + - + +
34J GLU* 3.0 54.6 + - + +
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Residues in contact with LYS 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E A 3.3 14.9 + - - +
17E T 2.9 35.6 + - - +
8F T 4.3 6.3 + - - -
9F T 3.7 40.1 + - - +
24I ARG* 4.7 10.1 + - - +
27I GLY 5.2 7.4 - - - +
28I LEU* 4.0 15.8 - - + +
31I LYS* 4.0 27.6 - - + +
27J GLY 3.1 18.1 + - - +
28J LEU* 3.3 5.8 + - + +
30J LYS* 1.3 72.6 - - - +
32J ALA* 1.3 59.6 + - - +
34J GLU* 3.4 12.5 + - - +
35J LEU* 3.0 30.5 + - - +
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Residues in contact with ALA 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU* 3.7 19.2 - - + +
45I LEU* 5.4 0.4 - - + -
28J LEU 3.0 12.7 + - - +
29J MET* 3.2 10.5 + - - +
31J LYS* 1.3 72.4 - - - +
33J TYR* 1.3 61.3 + - - +
35J LEU* 3.4 1.1 + - - -
36J SER* 2.9 26.7 + - - -
43J ILE* 3.5 21.0 - - + +
45J LEU* 4.6 6.3 - - + -
57J TYR* 3.6 26.7 - - + -
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Residues in contact with TYR 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ILE* 3.8 33.7 + - + +
81I ASN* 3.4 28.9 - - + +
84I ILE* 4.1 23.1 - - + -
85I LEU* 3.1 44.6 - - + +
88I LEU* 4.4 16.4 - - + -
29J MET 2.9 16.4 + - - +
30J LYS* 3.5 8.7 - - + +
31J LYS 3.3 0.2 - - - -
32J ALA* 1.3 76.2 - - - +
34J GLU* 1.3 71.5 + - + +
36J SER* 2.7 18.2 + - - -
37J VAL* 3.0 24.7 + - + +
57J TYR* 3.3 12.0 + - - +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F T 5.2 1.6 - - - +
9F T 4.4 7.7 + - - -
8I ILE* 3.6 38.9 - - + +
24I ARG* 3.0 30.9 + - - +
30J LYS* 3.0 47.5 + - - +
31J LYS* 3.8 8.5 + - - +
32J ALA 3.3 0.2 - - - -
33J TYR* 1.3 88.0 - - + +
35J LEU* 1.3 60.8 + - - +
37J VAL* 3.3 1.2 + - - +
38J LEU* 2.8 37.5 + - + +
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I PHE* 4.0 22.7 - - + +
24I ARG* 3.9 27.2 - - + +
25I LYS* 4.1 20.0 - - + +
28I LEU* 3.9 24.2 - - + -
47I ILE* 4.3 9.2 - - + -
31J LYS 3.0 17.7 + - - +
32J ALA* 3.7 4.3 - - - +
34J GLU* 1.3 77.1 - - - +
36J SER* 1.3 62.4 - - - +
38J LEU* 4.6 4.0 - - - +
39J CYS* 3.0 47.6 + - - +
40J ASP 4.1 0.2 + - - -
41J CYS* 4.4 3.3 - - - -
43J ILE* 3.9 12.8 - - + -
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Residues in contact with SER 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ASN* 3.7 9.0 + - - -
32J ALA 2.9 14.1 + - - -
33J TYR* 2.7 19.6 + - - -
35J LEU* 1.3 75.5 - - - +
37J VAL* 1.3 58.0 + - - +
40J ASP* 3.1 10.0 + - - -
41J CYS* 3.0 46.9 + - - +
43J ILE* 3.9 6.9 - - - +
57J TYR* 3.6 2.4 + - - -
59J SER* 3.5 26.9 - - - -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ILE* 3.7 15.0 - - + +
9I THR* 3.7 29.6 - - - +
10I ARG* 3.2 23.7 - - - +
81I ASN* 4.7 6.3 - - - +
33J TYR* 3.0 40.1 + - + +
34J GLU 3.9 2.5 - - - +
36J SER* 1.3 82.2 - - - +
38J LEU* 1.3 66.2 + - - +
39J CYS 3.3 0.3 + - - -
40J ASP* 3.6 3.6 + - - -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 3.9 17.0 - - + -
7I GLN 3.6 19.1 - - - +
8I ILE* 4.1 11.7 - - + -
9I THR 3.4 23.1 - - - +
10I ARG* 3.7 1.0 - - - +
11I ILE* 2.9 49.7 + - + +
17I ARG* 4.2 1.4 - - - +
20I THR* 4.5 3.6 - - + -
24I ARG* 3.5 45.1 - - - +
34J GLU 2.8 25.7 + - - +
35J LEU* 4.2 0.9 - - - +
37J VAL* 1.3 72.1 - - - +
39J CYS* 1.3 66.9 + - - +
40J ASP 3.9 0.2 + - - -
----------------------------------------------------------
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Residues in contact with CYS 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 4.8 0.7 - - - -
17I ARG* 3.6 45.5 - - + -
20I THR* 4.0 13.7 - - - -
21I PHE* 3.6 39.4 - - + -
49I ASN* 5.5 0.7 - - - +
50I SER* 4.1 5.9 + - - -
35J LEU* 3.0 24.5 + - + +
38J LEU* 1.3 83.1 - - - +
40J ASP* 1.3 71.6 - - - +
41J CYS* 3.4 7.5 + - - -
----------------------------------------------------------
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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