Contacts of the helix formed by residues 4 - 35 (chain D) in PDB entry 3E1J
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 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLY* 1.3 71.7 - - - -
5D THR* 1.3 65.7 + - - +
6D LYS* 3.0 6.3 + - - +
7D VAL* 2.9 45.5 + - + +
8D ILE* 3.2 20.7 + - - +
65D LEU* 5.4 0.8 - - - +
107D TYR* 2.9 26.9 + - - -
111D VAL* 3.8 19.0 - - + +
113D ASP* 5.5 2.9 + - + +
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Residues in contact with THR 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LYS* 4.7 12.6 + - - -
3D GLY 3.5 3.6 + - - -
4D ASP* 1.3 74.2 + - - +
6D LYS* 1.3 59.0 + - - +
8D ILE* 3.2 14.3 + - + +
9D ASN* 2.9 39.9 + - - +
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Residues in contact with LYS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 3.0 10.7 + - - +
5D THR* 1.3 76.2 - - - +
7D VAL* 1.3 65.6 + - - +
9D ASN* 3.2 18.5 + - + +
10D TYR* 2.9 51.5 + - + -
103D GLU* 5.1 1.4 + - - -
107D TYR* 3.4 32.4 - - + +
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 2.9 31.6 + - + +
6D LYS* 1.3 76.3 - - - +
8D ILE* 1.3 56.9 + - - +
10D TYR* 3.2 8.7 + - + +
11D LEU* 2.8 48.1 + - + +
65D LEU* 4.2 4.3 - - + -
107D TYR* 3.7 10.9 - - + -
108D ALA* 4.4 7.9 - - + -
111D VAL* 3.7 24.2 - - + -
113D ASP* 3.4 28.9 - - + +
116D SER* 4.1 7.6 - - - +
120D MET* 5.8 0.9 - - + -
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Residues in contact with ILE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLY 4.4 7.9 - - - +
4D ASP 3.2 14.5 + - - +
5D THR* 3.2 12.8 + - + +
7D VAL* 1.3 77.8 - - - +
9D ASN* 1.3 58.5 + - - +
11D LEU* 3.2 7.5 + - - +
12D ASN* 2.9 37.3 + - - +
62D ILE* 4.0 25.1 - - + +
65D LEU* 3.6 44.0 - - + +
66D GLU 4.6 1.1 - - - +
67D GLY* 4.1 19.5 - - - +
68D LEU 4.7 1.1 - - - +
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Residues in contact with ASN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 2.9 33.3 + - - +
6D LYS* 3.2 22.5 + - + +
8D ILE* 1.3 76.9 - - - +
10D TYR* 1.3 57.7 + - + +
12D ASN* 3.2 9.0 + - - +
13D LYS* 2.9 28.9 + - - +
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Residues in contact with TYR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LYS* 2.9 46.1 + - + -
7D VAL* 3.4 8.7 - - + +
9D ASN* 1.3 77.6 - - + +
11D LEU* 1.3 54.9 + - + +
13D LYS* 3.0 19.8 + - + +
14D LEU* 2.8 41.8 + - + +
100D ASN* 4.8 4.0 - - + -
103D GLU* 2.6 49.8 + - + +
104D ALA* 3.7 33.2 - - + -
107D TYR* 3.8 39.4 - + + +
120D MET* 6.2 0.2 - - + -
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 2.8 33.6 + - + +
8D ILE* 3.2 6.5 + - - +
10D TYR* 1.3 72.9 - - + +
12D ASN* 1.3 56.2 + - - +
14D LEU* 3.4 4.8 + - + +
15D LEU* 2.8 30.1 + - - +
58D TYR* 4.1 24.7 - - + +
61D ARG* 3.8 27.8 - - + -
62D ILE* 3.6 24.9 - - + +
65D LEU* 3.9 19.5 - - + -
116D SER* 4.2 4.9 - - - +
119D MET* 5.5 1.3 - - - -
120D MET* 4.0 30.1 - - + -
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Residues in contact with ASN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 2.9 28.7 + - - +
9D ASN* 3.7 7.6 + - - +
10D TYR 3.2 0.2 - - - -
11D LEU* 1.3 75.1 - - - +
13D LYS* 1.3 58.0 + - - +
15D LEU* 3.3 7.1 + - - +
16D GLY* 2.8 25.5 + - - -
62D ILE* 3.3 17.6 - - - +
68D LEU 3.0 22.8 + - - -
70D ASN* 2.7 43.1 + - + +
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Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASN 2.9 15.1 + - - +
10D TYR* 3.0 23.8 + - + +
12D ASN* 1.3 77.4 - - - +
14D LEU* 1.3 64.3 + - + +
16D GLY* 3.1 5.0 + - - -
17D ASN* 3.0 23.1 + - - +
100D ASN* 3.5 43.3 + - + +
103D GLU* 5.7 3.4 - - - -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 2.8 25.1 + - + +
11D LEU* 3.7 3.1 - - + +
13D LYS* 1.3 68.9 - - + +
15D LEU* 1.3 68.0 + - - +
17D ASN* 2.9 22.0 + - - +
18D GLU* 3.0 15.2 + - - +
58D TYR* 3.5 33.7 - - + +
100D ASN* 3.6 33.7 - - + +
101D LEU* 3.8 24.7 - - + +
104D ALA* 3.9 11.7 - - + -
120D MET* 3.6 31.0 - - - -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU 2.8 21.4 + - - +
12D ASN* 3.4 17.5 - - - +
13D LYS 3.3 0.2 - - - -
14D LEU* 1.3 70.0 - - - +
16D GLY* 1.3 57.9 + - - +
18D GLU* 3.1 2.4 + - - +
19D LEU* 2.9 48.9 + - + +
55D ALA* 3.7 40.6 - - + +
58D TYR* 3.8 14.9 - - + -
59D ILE* 3.9 21.8 - - + -
62D ILE* 4.3 4.9 - - + -
69D PRO* 4.2 3.8 - - + -
70D ASN 3.8 23.3 - - - +
71D LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN 2.8 14.5 + - - -
13D LYS* 3.1 6.4 + - - -
15D LEU* 1.3 76.7 - - - +
17D ASN* 1.3 61.6 + - - +
19D LEU* 3.3 14.7 + - - +
20D VAL* 3.2 28.1 + - - +
70D ASN 5.3 1.8 + - - -
73D ASP 5.1 5.5 - - - +
74D LEU* 5.1 0.5 - - - +
75D GLY 5.2 0.9 + - - -
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS* 3.0 18.7 + - - +
14D LEU* 2.9 16.6 + - - +
16D GLY* 1.3 76.7 - - - +
18D GLU* 1.3 64.0 + - + +
20D VAL* 3.3 10.5 + - - +
21D ALA* 3.0 21.9 + - - +
93D LEU* 5.0 8.3 - - + +
96D ASP* 6.4 0.2 - - - -
97D GLY* 3.6 24.9 - - - -
100D ASN* 2.9 35.4 + - - +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.0 16.6 + - - +
15D LEU 3.7 5.2 - - - +
17D ASN* 1.3 77.5 - - - +
19D LEU* 1.3 59.2 + - - +
21D ALA* 3.2 4.2 + - - +
22D ILE* 2.8 35.5 + - - +
51D GLU* 2.9 48.9 - - - +
54D HIS* 3.3 19.1 + - + +
55D ALA* 4.3 8.1 - - + +
58D TYR* 3.7 20.5 + - + -
101D LEU* 5.2 2.6 - - - +
123D ILE* 3.7 11.3 - - - +
127D GLU* 2.7 20.9 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN* 4.8 4.9 - - - +
200C HEM 3.7 32.1 - - + -
15D LEU* 2.9 54.3 + - + +
16D GLY* 3.5 18.4 - - - +
17D ASN 3.2 0.4 - - - -
18D GLU* 1.3 79.4 - - - +
20D VAL* 1.3 62.6 + - - +
22D ILE* 3.7 5.9 + - + +
23D ASN* 3.6 18.4 + - - -
55D ALA* 4.7 3.6 - - + -
70D ASN 4.3 9.9 - - - +
71D LEU* 4.0 24.9 - - + +
73D ASP 4.5 11.7 - - - +
74D LEU* 3.8 17.8 - - + +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY 3.2 19.0 + - - +
17D ASN* 3.9 7.0 - - - +
19D LEU* 1.3 75.5 - - - +
21D ALA* 1.3 58.1 + - - +
23D ASN* 3.2 4.9 + - - +
24D GLN* 2.9 27.9 + - - +
74D LEU* 3.8 8.4 - - + +
75D GLY* 3.9 28.5 - - - +
76D LYS 3.9 14.6 - - - +
77D LEU* 3.7 25.8 - - + +
93D LEU* 3.7 26.7 - - + -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN 3.0 14.2 + - - +
18D GLU* 3.2 9.4 + - - +
20D VAL* 1.3 76.2 - - - +
22D ILE* 1.3 54.9 + - - +
24D GLN* 4.4 1.1 - - - +
25D TYR* 2.8 48.8 + - + +
51D GLU* 3.8 25.6 - - + +
93D LEU* 3.8 21.3 - - + -
94D GLU* 5.6 1.6 - - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C HEM 3.8 45.8 - - + -
18D GLU 2.8 23.6 + - - +
19D LEU* 3.8 6.3 - - - +
20D VAL 3.3 0.2 - - - -
21D ALA* 1.3 72.1 - - - +
23D ASN* 1.3 70.6 + - - +
26D PHE* 3.1 16.3 + - - +
48D SER* 2.8 31.4 + - - +
51D GLU* 3.6 12.3 - - + +
52D MET* 3.6 45.8 - - + +
55D ALA* 4.1 11.4 - - + -
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.9 5.9 - - - +
71C LEU* 3.5 45.2 - - + +
200C HEM 3.0 35.6 - - - +
19D LEU 3.6 11.2 + - - +
20D VAL 3.2 7.2 + - - +
22D ILE* 1.3 79.3 - - - +
24D GLN* 1.3 69.2 + - - +
26D PHE* 3.3 1.8 + - - +
27D LEU* 3.0 26.0 + - - +
74D LEU* 3.8 12.3 - - - +
77D LEU* 4.4 10.1 - - + -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 2.9 19.3 + - - +
21D ALA* 4.0 2.5 - - - +
23D ASN* 1.3 77.5 - - - +
25D TYR* 1.3 58.4 + - - +
27D LEU* 3.9 0.9 - - - +
28D HIS* 3.0 46.1 + - + +
76D LYS 4.8 0.5 - - - +
77D LEU* 3.8 14.1 - - + +
78D ASN* 3.0 34.4 + - - +
79D ILE* 4.4 9.0 - - + -
89D SER* 3.1 24.5 + - - -
90D ASP* 2.9 33.9 + - - +
93D LEU* 4.0 19.0 - - + +
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Residues in contact with TYR 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 2.8 28.7 + - + +
24D GLN* 1.3 78.1 - - + +
26D PHE* 1.3 57.1 + - - +
28D HIS* 3.4 1.7 + - - +
29D ALA* 2.8 30.1 + - - +
44D GLU* 3.4 39.2 - - - +
47D GLU* 3.6 34.3 + - + -
48D SER* 3.8 9.4 - - - +
51D GLU* 3.9 25.4 - - + -
90D ASP* 3.5 30.0 - - + +
93D LEU* 6.1 2.5 - - + -
94D GLU* 2.4 41.7 + - + +
130D HIS* 4.0 3.5 - - - +
134D LEU* 3.6 12.4 - - + +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 3.4 42.2 - - + -
59C ILE* 3.9 13.9 - - + -
71C LEU* 5.2 1.6 - - + -
200C HEM 3.5 55.2 - + + -
22D ILE 3.1 18.9 + - - +
23D ASN* 3.8 4.3 - - - +
25D TYR* 1.3 74.3 - - - +
27D LEU* 1.3 65.0 + - - +
29D ALA* 3.3 6.2 + - + +
30D ARG* 3.0 38.7 + - + +
45D TYR* 3.6 28.0 - + - -
48D SER* 3.6 19.2 + - - +
52D MET* 4.6 0.4 - - + -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 4.4 5.2 - - + -
63C LEU* 4.3 6.1 - - + -
69C PRO* 3.9 43.3 - - + +
71C LEU* 4.0 23.0 - - + +
23D ASN 3.0 15.7 + - - +
24D GLN 4.0 2.7 - - - +
26D PHE* 1.3 76.7 - - - +
28D HIS* 1.3 65.5 + - + +
30D ARG* 3.2 3.9 + - - +
31D MET* 2.9 39.7 + - + +
77D LEU* 5.6 0.9 - - + -
79D ILE* 3.6 43.7 - - + -
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 3.0 32.6 + - + +
25D TYR 3.7 0.2 - - - +
27D LEU* 1.3 76.0 - - - +
29D ALA* 1.3 64.7 + - - +
31D MET* 3.1 3.6 + - - +
32D PHE* 2.9 32.4 + + + -
44D GLU* 3.1 16.2 - - - +
78D ASN 4.4 1.1 - - - -
79D ILE* 2.7 42.7 + - + -
86D MET* 3.2 47.9 + - + +
90D ASP* 2.7 37.0 + - - -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR 2.8 17.6 + - - +
26D PHE* 3.4 8.1 - - + +
28D HIS* 1.3 76.7 - - - +
30D ARG* 1.3 60.2 + - + +
32D PHE* 3.3 5.4 + - - +
33D LYS 2.9 21.8 + - - -
41D ASN* 3.0 26.4 - - - +
44D GLU* 3.9 7.9 - - + +
45D TYR* 3.6 33.2 - - + +
----------------------------------------------------------
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 2.7 46.8 + - - -
59C ILE* 4.1 10.8 - - + -
60C GLU* 3.0 32.4 + - + +
63C LEU* 3.7 20.9 - - + +
26D PHE* 3.0 35.3 + - + +
27D LEU 4.1 0.4 - - - +
29D ALA* 1.3 73.2 - - + +
31D MET* 1.3 60.3 + - - +
33D LYS* 3.6 13.4 - - + +
34D ASN* 2.9 28.4 + - - +
41D ASN* 3.4 30.5 + - - +
45D TYR* 3.3 35.5 - - - -
----------------------------------------------------------
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Residues in contact with MET 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 4.2 17.5 - - + -
27D LEU* 2.9 33.4 + - + +
28D HIS* 3.4 9.0 - - - +
30D ARG* 1.3 74.0 - - - +
32D PHE* 1.3 66.4 + - - +
34D ASN* 3.1 6.9 + - - +
35D TRP* 2.9 49.0 + - + -
79D ILE* 3.7 23.1 - - + -
80D GLY 3.8 16.2 - - - +
81D GLU* 4.9 2.2 - - - +
86D MET* 3.7 33.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 2.9 24.6 + - + -
29D ALA 3.4 7.0 - - - +
31D MET* 1.3 74.7 - - - +
33D LYS* 1.3 61.2 + - - +
35D TRP* 3.2 14.3 + + - -
36D GLY 3.0 4.2 + - - -
37D LEU* 2.8 39.5 + - + +
40D LEU* 3.7 37.5 - - + -
41D ASN 3.9 12.3 - - - +
44D GLU* 3.9 26.9 - - + -
83D VAL* 4.0 20.6 - - + -
86D MET* 3.4 38.8 - - + -
87D LEU* 3.9 17.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU* 3.4 29.8 - - + -
29D ALA 2.9 7.5 + - - +
30D ARG* 3.6 20.2 - - - +
31D MET 3.2 0.4 - - - -
32D PHE* 1.3 71.4 - - - +
34D ASN* 1.3 68.6 + - - +
36D GLY* 2.9 15.0 + - - -
37D LEU 4.8 2.7 - - - +
38D LYS* 5.4 4.2 - - + +
41D ASN* 3.5 39.7 - - - +
----------------------------------------------------------
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU 5.2 1.4 + - - -
63C LEU* 4.2 25.5 - - + +
64C PHE* 4.0 26.1 - - - +
30D ARG 2.9 18.4 + - - +
31D MET 3.1 5.4 + - - +
33D LYS* 1.3 79.8 - - - +
35D TRP* 1.3 72.1 + - + +
36D GLY 3.2 1.4 + - - -
132H ASP* 4.0 17.7 + - - +
136H THR* 3.5 20.1 + - - +
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Residues in contact with TRP 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D MET* 2.9 34.7 + - + -
32D PHE* 3.2 22.4 + + - +
34D ASN* 1.3 87.0 + - - +
36D GLY* 1.3 60.1 + - - +
37D LEU* 3.5 18.3 + - + +
81D GLU 3.4 25.6 - - - -
82D ASP* 4.3 2.0 - - - -
83D VAL* 4.4 11.0 - - + -
86D MET* 3.7 32.8 - - + -
136H THR* 3.5 12.9 - - - +
139H ASP* 5.6 3.6 - - + -
140H LEU* 3.5 18.7 - - - +
143H LYS* 3.8 33.5 + - - +
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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