Contacts of the helix formed by residues 9 - 38 (chain C) in PDB entry 2CHP
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 ASN 9 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 1.3 65.5 + - - +
11C THR* 3.4 4.9 - - - +
12C LEU* 3.4 28.9 + - - +
13C VAL* 3.1 27.2 + - - +
121C LEU* 5.2 1.0 - - - +
124C GLU* 4.2 34.0 + - - +
125C ASN* 3.1 30.4 - - + +
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Residues in contact with GLN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 1.3 78.2 - - - +
11C THR* 1.3 65.5 + - - +
13C VAL* 3.3 7.6 + - - +
14C GLU* 2.8 61.9 + - - +
71C ILE* 3.2 35.0 + - - +
125C ASN* 3.1 27.4 - - - +
127C ASP* 5.5 1.7 - - - +
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Residues in contact with THR 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN 3.4 2.8 - - - +
10C GLN* 1.3 81.5 - - - +
12C LEU* 1.3 58.3 + - + +
14C GLU* 3.3 11.5 + - - +
15C ASN* 2.9 47.9 + - - +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 3.4 31.4 + - - +
10C GLN 3.3 0.2 - - - -
11C THR* 1.3 78.4 - - + +
13C VAL* 1.3 64.8 + - - +
15C ASN* 3.9 9.4 - - + +
16C SER* 3.0 25.8 + - - -
121C LEU* 3.9 30.1 - - + +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN 3.1 16.6 + - - +
10C GLN* 3.3 10.5 + - - +
12C LEU* 1.3 74.9 - - - +
14C GLU* 1.3 63.1 - - - +
16C SER* 2.8 22.0 + - - +
17C LEU* 3.0 26.6 + - + +
71C ILE* 4.1 19.7 - - + -
118C VAL* 5.6 1.3 - - + -
121C LEU* 3.8 35.7 - - + +
122C ALA* 4.0 8.1 - - + +
125C ASN* 4.2 12.8 - - + +
127C ASP* 4.6 5.4 - - - +
130C THR* 4.2 11.4 - - + -
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 2.8 54.3 + - - +
11C THR* 3.3 10.1 + - - +
13C VAL* 1.3 76.7 - - - +
15C ASN* 1.3 66.9 + - - +
17C LEU* 3.2 5.0 + - - +
18C ASN* 3.0 27.9 + - - +
68C LEU* 3.8 25.7 - - + +
71C ILE* 4.5 2.9 - - + -
72C GLY 4.0 5.3 - - - +
73C GLY* 3.8 24.4 + - - -
74C GLN 4.9 0.9 + - - +
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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 THR* 2.9 40.5 + - - +
12C LEU* 3.9 9.8 - - + +
14C GLU* 1.3 78.1 - - - +
16C SER* 1.3 61.4 + - - +
18C ASN* 3.2 11.3 + - - +
19C THR* 3.1 24.5 + - - -
85C HIS* 5.5 1.6 + - - -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 3.0 16.1 + - - -
13C VAL* 2.8 20.6 + - - -
15C ASN* 1.3 74.7 - - - +
17C LEU* 1.3 64.1 + - - +
19C THR* 3.4 8.0 + - - -
20C GLN* 3.1 28.8 + - - +
117C PHE* 5.8 1.8 - - - -
118C VAL* 3.8 31.0 - - - +
121C LEU* 3.9 14.9 - - - +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 3.0 22.4 + - + +
14C GLU 3.2 7.4 + - - +
16C SER* 1.3 76.7 + - - +
18C ASN* 1.3 58.5 + - - +
20C GLN* 3.3 4.1 + - - +
21C LEU* 2.7 31.4 + - - +
64C ILE* 3.6 16.5 - - + +
67C ARG* 4.4 7.0 - - + -
68C LEU* 4.0 39.9 - - + +
71C ILE* 4.2 11.4 - - + -
118C VAL* 3.9 13.5 - - + -
130C THR* 3.8 26.5 - - + -
134C PHE* 3.8 28.9 - - + -
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Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 3.0 13.4 + - - +
15C ASN* 3.2 12.3 + - - +
17C LEU* 1.3 76.2 - - - +
19C THR* 1.3 59.3 + - - +
21C LEU* 3.6 7.1 - - - +
22C SER* 2.8 31.6 + - - -
68C LEU* 3.4 12.6 - - - +
74C GLN 3.1 16.5 - - - +
75C PRO* 3.3 10.1 - - - +
76C VAL* 2.9 43.1 + - + +
85C HIS* 4.4 18.0 + - + +
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN 3.1 14.1 + - - -
16C SER* 3.6 11.0 - - - -
18C ASN* 1.3 75.9 - - - +
20C GLN* 1.3 73.3 + - - +
22C SER* 3.4 4.3 + - - -
23C ASN* 2.9 29.8 + - - +
85C HIS* 3.3 29.1 + - - +
87C SER* 4.1 21.1 - - - +
114C GLU* 4.4 1.1 - - - +
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 3.1 18.8 + - - +
17C LEU 3.9 2.2 - - - +
19C THR* 1.3 80.9 - - - +
21C LEU* 1.3 66.9 + - - +
23C ASN* 3.1 22.7 + - - +
24C TRP* 3.0 33.0 + - + -
64C ILE* 4.2 5.6 - - + -
111C ILE* 4.2 21.3 - - - +
114C GLU* 3.0 41.5 + - - +
115C SER* 4.4 3.8 + - - +
118C VAL* 4.2 11.7 - - + +
134C PHE* 4.0 30.7 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU 2.7 21.4 + - - +
18C ASN* 3.6 15.3 - - - +
20C GLN* 1.3 72.1 - - - +
22C SER* 1.3 56.4 + - - +
24C TRP* 3.2 4.0 + - - +
25C PHE* 2.9 28.1 + - - +
61C VAL* 3.4 45.5 - - + +
64C ILE* 3.9 14.6 - - + +
65C ALA* 4.1 12.3 - - + +
68C LEU* 5.2 1.1 - - + -
75C PRO* 3.6 22.9 - - + -
76C VAL* 3.4 25.4 - - + +
82C TYR* 4.3 9.6 - - + -
36D TRP* 4.2 7.2 - - + -
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN 2.8 22.3 + - - -
19C THR 3.5 4.9 - - - -
21C LEU* 1.3 71.6 - - - +
23C ASN* 1.3 60.5 + - - +
25C PHE* 3.3 2.6 + - - +
26C LEU* 2.9 34.3 + - - +
76C VAL* 3.5 9.4 - - - +
82C TYR* 3.4 40.4 - - - +
85C HIS* 3.4 13.5 - - - +
86C ALA* 3.5 13.0 - - - -
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 2.9 13.2 + - - +
20C GLN* 3.1 39.7 + - - +
22C SER* 1.3 74.5 - - - +
24C TRP* 1.3 58.9 + - + +
26C LEU 3.2 1.4 + - - -
27C LEU* 2.9 29.8 + - - +
86C ALA* 3.4 2.5 - - - +
87C SER* 2.8 45.2 + - - -
88C ILE* 3.2 31.2 + - + +
111C ILE* 4.4 16.5 - - + +
114C GLU* 3.4 2.8 + - - -
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Residues in contact with TRP 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 3.0 33.4 + - + +
21C LEU* 3.7 4.5 - - - +
23C ASN* 1.3 78.1 - - + +
25C PHE* 1.3 64.6 + - - +
27C LEU* 3.5 21.4 + - + +
28C TYR* 3.0 23.2 + - - +
56C HIS* 3.6 35.9 - + - -
57C ALA* 3.8 28.7 - - + +
60C THR* 3.6 16.0 - - + +
61C VAL* 3.7 21.4 - - + +
64C ILE* 3.6 17.2 - - + +
108C TYR* 4.0 10.8 - + - -
111C ILE* 3.8 26.5 - - + +
115C SER* 5.5 0.4 + - - -
134C PHE* 5.6 0.2 - - - -
137C LEU* 3.7 19.1 - - + +
141C VAL* 3.6 27.8 - - + -
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU 2.9 16.4 + - - +
22C SER 3.8 3.6 - - - +
24C TRP* 1.3 76.1 - - - +
26C LEU* 1.3 64.3 + - + +
28C TYR* 3.4 8.9 - + + +
29C SER* 3.1 18.9 + - - -
61C VAL* 3.6 25.4 - - + +
79C VAL* 4.1 8.5 - - + -
82C TYR* 3.4 50.9 - + + -
25D PHE* 3.5 35.2 - + - -
28D TYR* 3.9 30.1 - + - -
29D SER* 4.3 16.4 - - - -
32D HIS* 5.1 7.2 - + - -
79D VAL* 4.7 5.6 - - + -
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER 2.9 19.5 + - - +
23C ASN 3.8 3.1 - - - +
25C PHE* 1.3 78.1 - - + +
27C LEU* 1.3 57.0 + - - +
29C SER* 3.4 2.0 + - - -
30C LYS* 3.0 24.6 + - - +
82C TYR* 4.1 21.3 - - + +
83C THR* 4.3 11.4 - - + +
86C ALA* 3.5 26.7 - - + -
88C ILE* 3.7 22.0 - - + +
89C THR* 4.1 10.1 - - - +
90C ASP* 3.2 28.1 - - + +
79D VAL* 3.9 33.9 - - + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN 2.9 17.3 + - - +
24C TRP* 3.9 24.5 - - + +
25C PHE 3.3 0.2 - - - -
26C LEU* 1.3 75.3 - - - +
28C TYR* 1.3 53.6 + - - +
30C LYS* 3.2 7.1 + - + +
31C LEU* 2.8 48.6 + - + +
88C ILE* 4.2 6.9 - - + +
104C LEU* 4.1 22.0 - - + -
107C ASP* 3.7 32.5 - - + +
108C TYR* 3.4 40.6 - - + +
111C ILE* 4.2 9.2 - - + -
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TRP 3.0 14.9 + - - +
25C PHE* 3.4 18.6 - + - +
27C LEU* 1.3 74.0 - - - +
29C SER* 1.3 58.6 + - - +
31C LEU* 3.6 2.3 + - - +
32C HIS* 2.8 61.0 + + - -
54C TYR* 3.3 41.0 - + + -
55C ASP* 5.5 0.2 - - - -
57C ALA* 4.1 11.7 - - + +
58C ALA* 3.7 16.4 - - + +
61C VAL* 5.3 2.2 - - + -
25D PHE* 3.9 23.6 - + - -
28D TYR* 3.3 45.3 + + - -
58D ALA* 3.6 19.9 - - - +
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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 PHE 3.1 13.1 + - - -
26C LEU* 3.5 7.6 - - - -
27C LEU 3.3 0.2 - - - -
28C TYR* 1.3 74.3 - - - +
30C LYS* 1.3 64.0 + - - +
32C HIS* 3.1 19.3 + - - +
33C ARG 3.2 9.4 + - - -
90C ASP* 2.6 28.9 + - - -
25D PHE* 4.2 20.6 - - - -
77D ALA 3.9 13.8 + - - +
78D THR* 4.0 1.2 - - - -
79D VAL* 4.0 13.7 + - - +
82D TYR* 4.4 6.2 + - - -
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU 3.0 19.1 + - - +
27C LEU* 3.7 12.1 - - + +
29C SER* 1.3 73.6 + - - +
31C LEU* 1.3 57.6 + - - +
33C ARG* 3.2 18.5 + - - +
34C PHE* 3.1 58.8 + - + -
88C ILE* 5.4 0.7 - - - -
89C THR* 2.9 31.8 + - - +
90C ASP* 3.9 13.2 - - + +
91C GLY 4.0 13.3 + - - -
94C GLU* 5.0 2.4 + - - +
103C ALA* 4.9 10.4 - - + +
104C LEU* 4.7 2.2 - - + -
107C ASP* 2.7 35.4 + - - +
77D ALA 5.2 0.2 - - - -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.8 37.8 + - + +
28C TYR 3.8 0.7 - - - +
30C LYS* 1.3 76.6 - - - +
32C HIS* 1.3 55.7 + - - +
34C PHE* 3.5 3.8 + - + +
35C HIS* 2.9 28.4 + - - +
50C PHE* 3.9 20.0 - - + +
53C LEU* 3.7 48.5 - - + +
54C TYR* 3.7 21.8 - - + +
57C ALA* 4.3 5.2 - - + -
104C LEU* 3.7 36.3 - - + -
108C TYR* 4.2 4.9 - - - +
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Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 2.8 58.9 + + - -
29C SER* 3.1 11.2 + - - +
31C LEU* 1.3 71.6 - - - +
33C ARG* 1.3 64.7 + - - +
35C HIS* 3.2 5.9 + - - +
36C TRP* 2.9 67.2 + + + -
54C TYR* 3.5 43.3 - + - -
25D PHE* 5.0 5.6 - + + -
58D ALA* 5.3 4.9 + - - +
61D VAL* 4.3 12.7 - - + +
62D ASP* 5.4 3.3 - - + +
82D TYR* 4.9 2.9 - - - +
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER 3.2 8.1 + - - +
30C LYS* 3.2 15.5 + - - +
32C HIS* 1.3 76.6 - - - +
34C PHE* 1.3 75.2 + - + +
36C TRP* 3.3 3.1 + - - -
37C TYR* 2.9 46.9 + - + +
90C ASP 3.1 26.5 + - - -
91C GLY* 3.3 14.7 + - - -
92C GLY 3.4 15.2 + - - -
93C ASN* 4.8 0.2 - - - +
94C GLU* 2.9 41.0 + - - +
100C MET* 5.9 0.7 - - + -
77D ALA* 3.6 38.4 + - + +
78D THR* 4.2 9.1 - - - +
81D GLU* 5.9 0.2 - - - -
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Residues in contact with PHE 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS* 3.1 36.9 + - + +
31C LEU* 3.5 3.6 + - - +
32C HIS 3.3 0.2 - - - -
33C ARG* 1.3 104.7 - - + +
35C HIS* 1.3 61.3 + - - +
38C VAL* 3.0 36.9 + - - +
50C PHE* 3.5 21.3 - + + -
94C GLU* 3.7 24.0 - - + -
100C MET* 3.3 54.7 - - + -
103C ALA* 4.0 4.3 - - + -
104C LEU* 3.7 32.1 - - + -
----------------------------------------------------------
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Residues in contact with HIS 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU 2.9 19.1 + - - +
32C HIS* 3.4 6.1 - - - +
34C PHE* 1.3 77.0 - - - +
36C TRP* 1.3 76.4 + + - +
38C VAL* 3.9 6.7 - - - +
43C PHE* 4.8 1.2 - - - -
47C HIS* 2.7 77.4 + + - -
48C GLU* 5.4 0.2 - - - -
50C PHE* 3.6 14.5 - - + -
51C GLU* 3.6 26.9 + - + -
54C TYR* 3.4 19.7 + + + -
62D ASP* 3.4 24.6 + - - -
66D GLU* 3.4 12.8 + - - -
----------------------------------------------------------
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Residues in contact with TRP 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 2.9 45.7 + + + +
33C ARG 3.8 1.8 - - - +
35C HIS* 1.3 94.1 - + - +
37C TYR* 1.3 68.5 + + + +
38C VAL 3.6 2.5 - - - +
43C PHE* 5.6 2.8 - - - -
47C HIS* 5.5 0.2 - - - -
21D LEU* 4.2 3.8 - - + -
61D VAL* 3.9 22.0 - - + -
62D ASP* 3.1 19.8 + - - -
65D ALA* 3.3 32.1 - - + +
66D GLU* 3.9 11.0 - - + -
69D LEU* 3.8 36.1 - - + +
75D PRO* 4.5 5.8 - - + -
76D VAL 3.6 14.4 - - - -
77D ALA* 3.7 18.4 - - + -
82D TYR* 3.4 26.7 - - - -
----------------------------------------------------------
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 2.9 37.1 + - + +
36C TRP* 1.3 84.8 - - + +
38C VAL* 1.3 67.6 + - - +
39C LYS* 3.4 12.3 + - - +
95C THR 4.9 1.7 - - - +
100C MET* 3.9 17.9 - - + +
69D LEU* 4.8 3.8 - - + -
74D GLN* 3.1 41.0 + - - +
75D PRO* 2.6 57.0 + - + -
77D ALA* 4.4 10.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PHE 3.0 21.7 + - - +
35C HIS 3.9 12.3 - - - +
36C TRP 3.6 1.2 - - - +
37C TYR* 1.3 79.5 - - - +
39C LYS* 1.3 71.2 + - - +
42C HIS 5.3 0.2 - - - -
43C PHE* 3.4 35.2 - - + +
46C LEU* 3.9 31.9 - - + -
47C HIS* 4.0 20.9 - - - +
50C PHE* 4.1 7.2 - - + -
95C THR 5.6 0.2 - - - -
97C ALA* 4.3 8.7 - - + +
100C MET* 3.9 15.4 - - - +
----------------------------------------------------------
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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