Contacts of the helix formed by residues 3 - 33 (chain C) in PDB entry 3BVI
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 3 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 1.3 73.5 - - - +
4C LYS* 1.3 66.5 + - - +
5C ASP* 3.9 5.8 + - - +
6C ILE* 3.3 26.0 + - - +
7C ILE* 3.0 24.1 + - - +
107C HIS* 5.0 1.6 + - - -
111C SER* 4.8 9.4 + - - -
113C ASP* 5.1 3.1 + - - +
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Residues in contact with LYS 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU 4.0 0.4 + - - -
3C SER* 1.3 73.2 - - - +
5C ASP* 1.3 60.9 + - - +
7C ILE* 3.5 14.1 - - + +
8C LYS* 3.0 27.7 + - - +
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Residues in contact with ASP 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.2 5.2 + - - +
4C LYS* 1.3 78.1 - - - +
6C ILE* 1.3 65.1 + - - +
8C LYS* 3.3 17.8 + - - +
9C LEU* 3.0 31.3 + - + +
107C HIS* 3.5 29.8 + - + +
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Residues in contact with ILE 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 3.8 16.8 - - + -
3C SER* 3.3 21.5 + - - +
5C ASP* 1.3 73.2 - - - +
7C ILE* 1.3 67.8 + - - +
9C LEU* 3.2 5.4 + - + +
10C LEU* 2.8 46.2 + - + +
104C ILE* 4.2 14.4 - - + +
107C HIS* 3.7 24.7 - - + -
108C ALA* 4.0 25.8 - - + +
111C SER* 4.3 5.4 - - - +
113C ASP* 3.8 20.6 - - + +
116C THR* 4.0 9.4 - - + +
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C PRO* 3.9 24.0 - - + -
2C LEU* 3.5 32.1 - - + +
3C SER 3.0 17.4 + - - +
4C LYS* 3.5 14.8 - - + +
6C ILE* 1.3 75.6 - - - +
8C LYS* 1.3 59.3 + - - +
10C LEU* 3.8 5.7 - - - +
11C ASN* 2.9 39.4 + - - +
61C LEU* 5.2 0.7 - - - +
66C VAL* 3.6 30.5 - - + -
67C PRO* 4.9 3.8 - - + +
69C GLN* 5.2 8.5 - - - +
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS 3.0 18.3 + - - +
5C ASP* 3.6 18.1 + - - +
6C ILE 3.2 0.2 - - - -
7C ILE* 1.3 79.3 - - - +
9C LEU* 1.3 73.4 + - - +
11C ASN* 3.9 4.3 - - - +
12C GLU* 3.0 63.6 + - + +
69C GLN* 6.3 0.9 - - - +
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASP* 3.0 21.7 + - + +
6C ILE* 3.7 4.9 - - + +
8C LYS* 1.3 89.0 - - - +
10C LEU* 1.3 56.8 + - - +
12C GLU* 3.4 20.5 + - - +
13C GLN* 3.0 27.7 + - - +
103C ASN* 3.8 20.6 - - - +
104C ILE* 3.9 33.8 - - + +
107C HIS* 3.7 38.6 - - + +
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 3.8 29.6 - - + -
6C ILE* 2.8 26.7 + - + +
7C ILE 3.9 2.7 - - - +
9C LEU* 1.3 74.7 - - - +
11C ASN* 1.3 59.0 + - - +
13C GLN* 3.2 6.0 + - + +
14C VAL* 3.0 31.8 + - - +
57C LEU* 4.8 14.8 - - + +
60C PHE* 3.9 18.2 - - + -
61C LEU* 3.8 21.5 - - + -
104C ILE* 4.1 25.8 - - + -
116C THR* 4.5 4.5 - - + -
120C LEU* 4.2 20.2 - - + -
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Residues in contact with ASN 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 2.9 30.2 + - - +
8C LYS* 3.9 4.5 - - - +
10C LEU* 1.3 74.1 - - - +
12C GLU* 1.3 64.4 + - + +
14C VAL* 3.2 6.6 + - - +
15C ASN* 2.8 31.1 + - - +
61C LEU* 3.6 14.1 - - - +
66C VAL* 4.3 0.2 - - - +
67C PRO 3.1 17.7 - - - +
68C VAL* 3.4 13.7 - - - +
69C GLN* 2.9 50.8 + - - +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 3.0 57.2 + - + +
9C LEU* 3.6 18.2 - - - +
11C ASN* 1.3 74.3 - - - +
13C GLN* 1.3 56.0 + - - +
15C ASN* 3.3 10.3 + - - +
16C LYS* 3.0 42.4 + - - +
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 3.0 13.5 + - - +
10C LEU* 3.4 11.0 - - + +
11C ASN 3.2 0.2 - - - -
12C GLU* 1.3 74.9 - - - +
14C VAL* 1.3 64.9 + - - +
16C LYS* 3.3 16.0 + - - +
17C GLU* 3.1 25.2 + - - +
57C LEU* 3.9 13.7 - - + -
97C ILE* 4.1 8.9 - - - +
100C SER* 3.2 31.0 + - - -
101C ILE* 3.6 14.3 - - - +
104C ILE* 3.5 26.9 - - + +
123C TYR* 3.1 30.4 + - + +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU 3.0 18.8 + - - +
11C ASN* 3.2 10.9 + - - +
13C GLN* 1.3 74.1 - - - +
15C ASN* 1.3 58.8 + - - +
17C GLU* 3.3 6.1 + - - +
18C MET* 3.1 30.7 + - + +
54C ALA* 4.1 4.7 - - + +
57C LEU* 3.7 30.7 - - + +
58C ILE* 3.9 26.0 - - + -
61C LEU* 4.1 19.1 - - + -
68C VAL* 4.8 1.8 - - + -
70C LEU* 3.8 27.1 - - + -
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Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 2.8 22.0 + - - +
12C GLU* 3.5 10.0 - - - +
13C GLN 3.2 0.4 - - - -
14C VAL* 1.3 77.4 - - - +
16C LYS* 1.3 59.3 + - - +
18C MET* 3.6 8.1 - - - +
19C ASN* 2.9 29.6 + - - +
69C GLN 3.2 21.2 + - - -
70C LEU* 3.5 16.1 - - - +
71C THR* 3.2 42.9 + - - +
73C ILE* 5.4 3.2 - - - +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU* 3.0 29.5 + - - +
13C GLN* 3.3 21.5 + - - +
15C ASN* 1.3 76.3 - - - +
17C GLU* 1.3 57.6 + - + +
19C ASN* 3.4 8.9 + - - +
20C SER* 2.9 32.4 + - - -
93C HIS* 5.2 0.7 - - - -
96C HIS* 3.8 27.3 + - + -
97C ILE* 4.5 13.8 - - + +
100C SER* 3.8 32.1 - - - +
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 3.1 16.3 + - - +
14C VAL 3.6 7.4 - - - +
16C LYS* 1.3 76.1 - - - +
18C MET* 1.3 59.6 + - - +
20C SER* 3.3 4.3 + - - -
21C SER* 3.0 29.5 + - - -
50C GLU* 2.9 48.0 - - - +
51C TYR* 5.7 0.2 - - - -
53C HIS* 3.9 14.6 - - + -
54C ALA* 3.9 11.9 - - + +
57C LEU* 4.3 4.7 - - + -
97C ILE* 3.9 9.8 - - - +
123C TYR* 2.3 33.7 + - - +
1006C FE 2.5 21.1 - - - -
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Residues in contact with MET 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 3.1 23.3 + - + +
15C ASN* 3.4 11.4 + - - +
17C GLU* 1.3 75.4 - - - +
19C ASN* 1.3 62.2 + - - +
21C SER* 3.4 5.3 + - - -
22C ASN* 3.2 26.0 + - - -
51C TYR* 3.6 40.4 - - + +
54C ALA* 3.8 17.7 - - + -
55C LYS 5.7 0.2 - - - +
58C ILE* 4.1 20.0 - - + -
70C LEU* 4.7 12.8 - - + -
73C ILE* 4.4 11.9 - - + -
22D ASN* 4.5 8.3 - - - +
25D MET* 4.9 7.6 - - + -
1008D GOL 3.7 26.4 + - - +
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN 2.9 18.6 + - - +
16C LYS* 3.6 7.6 - - - +
18C MET* 1.3 77.6 - - - +
20C SER* 1.3 56.2 + - - +
22C ASN* 3.2 13.4 + - - +
23C LEU* 3.0 29.3 + - - +
73C ILE* 4.7 6.7 - - + +
74C SER* 4.4 21.8 + - - +
76C PRO* 5.6 5.5 - - - +
93C HIS* 4.5 13.9 - - - -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS 2.9 21.9 + - - -
17C GLU* 3.3 8.7 + - - -
19C ASN* 1.3 74.1 - - - +
21C SER* 1.3 65.6 + - - +
23C LEU* 3.3 4.7 + - - +
24C TYR* 3.0 33.5 + - - -
50C GLU* 3.7 23.6 + - - -
93C HIS* 2.7 32.7 + - - -
97C ILE* 3.9 9.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU 3.0 13.3 + - - -
18C MET* 3.5 10.8 - - - -
20C SER* 1.3 76.0 - - - +
22C ASN* 1.3 62.6 + - - +
25C MET* 3.0 28.0 + - - +
47C ALA* 3.4 23.6 + - - +
50C GLU* 3.9 5.1 - - - +
51C TYR* 4.3 7.0 - - - -
18D MET* 5.7 0.2 - - - +
51D TYR* 2.8 33.4 + - - -
1008D GOL 4.2 7.1 + - - -
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Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET 3.2 7.9 + - - -
19C ASN* 3.4 12.4 - - - +
20C SER 3.2 0.6 - - - -
21C SER* 1.3 78.1 + - - +
23C LEU* 1.3 62.4 + - - +
25C MET* 3.3 2.5 + - - +
26C SER* 3.1 20.3 + - - -
73C ILE* 3.2 44.9 - - - +
74C SER 5.0 2.0 + - - +
76C PRO* 3.9 15.1 - - + +
18D MET* 4.6 10.6 - - - +
70D LEU* 3.4 29.9 - - + +
73D ILE* 5.6 1.0 - - - +
1008D GOL 3.7 20.5 + - - -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN* 3.0 17.7 + - - +
20C SER* 3.5 7.6 - - - +
22C ASN* 1.3 75.0 - - - +
24C TYR* 1.3 61.7 + - + +
26C SER* 3.2 4.9 + - - -
27C MET* 2.9 55.0 + - + +
76C PRO* 3.8 10.2 - - + +
77C GLU* 3.7 43.7 - - + +
80C PHE* 4.6 0.9 - - + -
89C LYS 5.8 0.4 - - - +
93C HIS* 4.0 40.6 - - + +
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 3.0 30.5 + - - +
23C LEU* 1.3 78.4 - - + +
25C MET* 1.3 57.6 + - - +
27C MET* 3.7 18.3 - - + +
28C SER* 2.8 30.3 + - - -
43C LEU* 3.7 31.7 - - + +
46C HIS* 3.4 21.3 - + - -
47C ALA* 3.7 10.5 - - + -
50C GLU* 4.0 9.9 - - + -
90C ALA* 3.4 33.1 + - + +
93C HIS* 3.5 21.1 - + - -
94C GLU* 2.6 41.0 + - - +
134C PHE* 4.0 9.3 - + - -
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Residues in contact with MET 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER* 3.0 21.7 + - - +
22C ASN 3.3 8.5 + - - +
24C TYR* 1.3 74.4 - - - +
26C SER* 1.3 57.5 + - - +
28C SER* 3.4 4.6 + - - -
29C SER* 3.0 28.1 + - - -
44C PHE* 3.6 45.8 - - + +
47C ALA* 3.7 15.9 - - + +
48C ALA 4.5 0.7 - - - +
18D MET* 5.1 4.3 - - + -
51D TYR* 3.6 24.0 - - + +
55D LYS* 4.0 15.7 - - + -
58D ILE* 4.1 29.3 - - + +
68D VAL* 5.0 5.5 - - + +
70D LEU* 3.8 15.7 - - + -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASN 3.1 11.7 + - - -
23C LEU 3.2 7.8 + - - -
25C MET* 1.3 74.0 - - - +
27C MET* 1.3 64.1 + - - +
29C SER* 3.4 6.9 + - - -
30C TRP* 3.1 22.7 + - - +
76C PRO* 3.9 14.4 - - - -
77C GLU 2.9 25.9 + - - -
78C HIS* 3.4 18.9 + - - +
80C PHE* 4.0 2.2 - - - -
68D VAL* 5.1 9.0 + - - -
70D LEU* 4.6 5.3 - - - +
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Residues in contact with MET 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 2.9 33.6 + - + +
24C TYR* 3.7 32.1 - - - +
26C SER* 1.3 73.6 - - - +
28C SER* 1.3 65.7 + - - +
30C TRP* 3.4 4.3 + - - +
31C CYS* 3.2 27.0 + - - -
43C LEU* 4.0 14.1 - - + -
77C GLU* 5.5 0.2 - - - +
80C PHE* 3.6 33.2 - - + -
86C ILE* 3.5 39.3 - - + +
89C LYS* 3.8 20.6 - - + -
90C ALA* 3.9 8.1 - - - +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR 2.8 19.0 + - - -
25C MET* 3.5 7.4 - - - -
27C MET* 1.3 77.0 - - - +
29C SER* 1.3 58.1 + - - +
31C CYS 3.4 1.2 + - - -
32C TYR* 3.0 36.0 + - - -
40C GLY* 2.6 32.9 + - - -
43C LEU* 3.8 9.1 - - - +
44C PHE* 3.4 25.1 - - - +
58D ILE* 6.5 0.2 - - - -
62D ASN* 4.4 3.3 + - - -
----------------------------------------------------------
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C MET 3.0 16.9 + - - -
26C SER* 3.7 7.6 - - - -
27C MET 3.2 0.2 - - - -
28C SER* 1.3 73.1 - - - +
30C TRP* 1.3 66.7 + - - +
32C TYR* 3.2 2.1 + - - +
33C THR* 2.9 27.2 + - - +
62D ASN* 4.0 11.3 + - - -
66D VAL 4.1 2.3 + - - -
67D PRO* 3.6 8.7 - - - +
68D VAL* 2.9 48.4 + - - +
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Residues in contact with TRP 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER 3.1 14.0 + - - +
27C MET 3.6 9.2 - - - +
28C SER 3.3 0.2 - - - -
29C SER* 1.3 76.5 - - - +
31C CYS* 1.3 67.0 + - - +
33C THR* 3.1 8.7 + - - -
34C HIS* 2.6 74.3 + + + -
36C LEU* 4.1 17.5 - - + -
78C HIS 4.0 9.9 - - - +
79C LYS* 5.0 0.2 - - - -
80C PHE* 3.1 56.8 + + + +
81C GLU 4.0 4.5 - - - -
82C GLY* 3.5 33.7 - - - -
83C LEU 4.4 0.2 - - - -
86C ILE* 3.5 16.2 - - + -
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Residues in contact with CYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET 3.2 13.8 + - - -
28C SER 3.6 5.2 - - - +
29C SER 3.3 0.2 - - - -
30C TRP* 1.3 86.3 - - - +
32C TYR* 1.3 60.9 + - - +
34C HIS 3.1 7.5 + - - +
36C LEU* 2.8 51.4 + - + +
39C ALA* 3.8 20.4 - - - -
40C GLY 3.6 10.5 - - - +
43C LEU* 3.9 12.3 - - - -
83C LEU* 4.4 9.4 - - - -
86C ILE* 3.9 16.2 - - - -
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Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 3.0 29.3 + - - +
29C SER 3.2 4.7 + - - +
31C CYS* 1.3 76.5 - - - +
33C THR* 1.3 62.1 + - + +
34C HIS 3.2 0.8 + - - -
35C SER* 3.8 8.0 + - - -
36C LEU 4.5 1.8 - - - -
37C ASP* 3.8 31.8 - - + +
40C GLY* 3.4 16.4 - - - -
41C LEU* 3.3 34.2 + - - +
44C PHE* 4.6 4.6 - + + +
62D ASN* 3.3 61.7 - - + +
63D GLU* 6.4 1.1 - - + -
65D ASN* 3.6 17.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER 2.9 20.3 + - - +
30C TRP* 3.1 10.2 + - - -
32C TYR* 1.3 78.0 - - + +
34C HIS* 1.3 75.9 + - - +
35C SER 3.6 1.3 - - - -
62D ASN* 6.1 1.1 - - - +
65D ASN* 3.7 39.1 + - - +
66D VAL 3.9 4.5 - - - +
67D PRO* 3.8 27.2 - - + +
1002D GLN 5.1 1.6 - - - +
1003D SER* 3.4 17.5 - - - -
----------------------------------------------------------
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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