Contacts of the helix formed by residues 11 - 43 (chain C) in PDB entry 1O9R
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 PRO 11 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP 3.7 5.6 - - - +
10C LEU* 1.4 100.7 - - + +
12C SER* 1.3 59.0 + - - +
13C ASN* 3.3 15.3 - - - +
14C ALA* 3.0 12.0 + - + +
15C LYS* 2.9 26.3 + - - +
132C GLY* 5.4 1.3 - - - +
122E ARG* 5.9 0.2 - - - -
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU 3.4 2.7 + - - -
11C PRO* 1.3 70.6 - - - +
13C ASN* 1.3 62.3 + - - +
15C LYS* 3.4 14.6 + - - +
16C SER* 3.1 25.5 + - - -
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Residues in contact with ASN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 3.9 13.7 - - - +
12C SER* 1.3 74.1 + - - +
14C ALA* 1.3 67.7 + - - +
16C SER* 3.5 7.7 + - - -
17C THR* 3.1 29.2 + - - +
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.8 24.5 - - + -
11C PRO* 3.0 19.3 + - + +
13C ASN* 1.3 78.4 + - - +
15C LYS* 1.3 67.0 + - - +
17C THR* 3.3 4.6 + - - -
18C VAL* 2.8 30.2 + - + +
131C ALA* 3.3 29.6 - - + +
132C GLY 5.2 0.4 - - - -
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C THR* 4.1 18.0 + - + +
8C ASN* 2.7 41.7 + - - +
9C ASP* 4.3 1.2 - - - +
10C LEU* 2.9 36.1 + - + +
11C PRO 2.9 16.7 + - - +
12C SER* 3.6 14.4 + - - +
13C ASN 3.3 0.2 - - - -
14C ALA* 1.3 76.2 - - - +
16C SER* 1.3 63.3 + - - +
18C VAL* 3.4 0.5 + - - +
19C ILE* 2.9 32.3 + - + +
76C LEU* 3.3 36.6 - - + +
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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 SER 3.1 14.2 + - - -
13C ASN* 3.6 11.9 - - - -
14C ALA 3.3 0.2 - - - -
15C LYS* 1.3 77.8 - - - +
17C THR* 1.3 63.3 + - - +
19C ILE* 3.5 8.2 + - - +
20C GLY* 3.3 17.8 + - - -
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASN* 3.1 16.8 + - - +
14C ALA* 3.8 5.6 - - - -
16C SER* 1.3 77.9 - - - +
18C VAL* 1.3 65.4 + - - +
20C GLY* 3.2 4.3 + - - -
21C ILE* 3.2 37.1 + - + +
127C ASP* 5.2 0.9 - - + +
131C ALA* 4.1 17.9 - - + -
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA 2.8 20.2 + - - +
15C LYS 4.2 1.6 - - - +
17C THR* 1.3 72.7 - - - +
19C ILE* 1.3 59.6 + - - +
21C ILE* 3.2 7.4 + - + +
22C LEU* 2.8 36.9 + - + +
76C LEU* 4.0 5.4 - - + -
128C SER* 4.2 13.0 - - - +
131C ALA* 3.9 24.7 - - + -
133C ASP* 3.6 27.8 - - + +
136C THR* 3.4 34.5 - - + +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS* 2.9 26.1 + - + +
16C SER* 3.9 7.0 - - - +
18C VAL* 1.3 76.8 - - - +
20C GLY* 1.3 58.8 + - - +
22C LEU* 3.4 7.5 + - - +
23C ASN* 2.9 45.7 + - - +
73C VAL* 3.9 17.3 - - + +
76C LEU* 3.6 38.6 - - + +
77C GLY 4.3 1.1 - - - -
78C GLY* 3.7 22.2 - - - +
79C THR 5.1 0.4 - - - +
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 3.3 7.3 + - - -
17C THR 3.2 7.9 + - - -
19C ILE* 1.3 76.1 - - - +
21C ILE* 1.3 61.3 + - - +
23C ASN* 4.1 3.7 - - - +
24C GLU* 2.9 31.4 + - - +
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Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.2 29.6 + - + +
18C VAL* 3.2 11.1 + - - +
20C GLY* 1.3 76.2 - - - +
22C LEU* 1.3 59.8 + - - +
24C GLU* 3.4 11.5 + - - +
25C SER* 3.0 29.7 + - - +
124C ALA* 3.7 32.1 - - + -
127C ASP* 3.7 38.8 - - + +
128C SER* 4.1 8.5 - - - +
140C PHE* 3.8 11.4 - - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 2.8 35.0 + - + +
19C ILE* 3.7 1.1 - - - +
21C ILE* 1.3 78.4 - - - +
23C ASN* 1.4 57.6 + - - +
25C SER* 3.2 1.6 + - - -
26C LEU 2.8 25.3 + - - -
69C ILE* 3.3 38.9 - - + +
72C ARG* 3.6 27.8 - - + -
73C VAL* 3.4 28.7 - - + +
76C LEU* 4.3 4.0 - - + -
136C THR* 3.9 10.5 - - + -
139C ILE* 5.0 3.1 - - + -
140C PHE* 3.6 27.4 - - + -
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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 ILE* 2.9 26.5 + - - +
20C GLY* 4.3 3.4 - - - +
22C LEU* 1.4 74.6 - - - +
24C GLU* 1.3 62.8 + - - +
26C LEU* 3.7 9.9 - - - +
27C ALA* 3.2 22.5 + - - +
73C VAL* 3.6 16.9 - - - +
79C THR 3.0 22.0 + - - -
80C ALA* 3.6 5.7 - - - -
81C LEU* 2.9 49.0 + - + +
90C THR* 4.1 4.5 - - + +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLY 2.9 19.8 + - - +
21C ILE* 3.7 10.1 - - - +
22C LEU 3.2 0.2 - - - -
23C ASN* 1.3 80.2 - - - +
25C SER* 1.3 64.7 + - - +
27C ALA* 3.3 10.2 + - - +
28C SER* 3.5 12.3 + - - -
90C THR* 4.0 18.7 - - + +
92C LYS* 3.6 31.6 + - + -
120C MET* 4.4 18.9 - - - +
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.0 17.6 + - - +
22C LEU 3.7 3.6 - - - -
24C GLU* 1.3 77.5 + - - +
26C LEU* 1.3 65.1 + - - +
28C SER* 3.2 2.9 + - - -
29C VAL* 2.9 28.1 + - - +
69C ILE* 4.5 3.6 - - - -
120C MET* 3.8 21.9 - - - +
121C ILE* 3.6 22.8 - - - +
124C ALA* 4.2 5.0 - - - +
140C PHE* 3.6 22.4 - - - -
----------------------------------------------------------
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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 LEU 2.8 21.5 + - - +
23C ASN* 3.7 18.8 - - - +
25C SER* 1.3 72.8 - - - +
27C ALA* 1.4 62.5 + - - +
29C VAL* 3.2 4.1 + - - +
30C ILE* 2.9 48.7 + - + +
66C GLY* 3.5 36.3 - - - +
69C ILE* 3.9 10.2 - - + +
70C ALA* 3.8 24.9 - - + -
80C ALA* 4.4 1.1 - - + -
81C LEU 3.7 28.0 - - - +
82C GLY* 4.3 4.3 - - - +
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN 3.2 6.9 + - - +
24C GLU 3.7 1.3 - - - +
25C SER 3.2 0.6 - - - -
26C LEU* 1.4 80.9 - - - +
28C SER* 1.3 58.9 + - - +
31C ASP* 3.0 23.9 + - - +
81C LEU 5.0 4.2 + - - +
86C ALA 4.3 1.3 - - - +
87C VAL* 3.4 30.6 - - + +
90C THR* 3.5 39.3 - - + -
91C THR* 3.8 10.7 - - - +
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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 GLU 3.5 4.1 + - - -
25C SER 3.2 2.9 + - - -
27C ALA* 1.3 75.6 - - - +
29C VAL* 1.3 61.1 + - - +
31C ASP* 3.7 1.2 - - - +
32C LEU* 2.9 29.3 + - - +
91C THR* 3.8 9.4 + - - -
92C LYS* 3.0 30.7 + - - +
93C LEU* 3.9 7.2 + - - +
117C VAL* 4.0 13.1 - - - +
120C MET* 3.7 36.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER 2.9 23.7 + - - +
26C LEU* 3.7 6.1 - - - +
28C SER* 1.3 74.8 - - - +
30C ILE* 1.3 62.2 - - + +
32C LEU* 3.3 8.3 + - - +
33C ALA* 2.9 26.3 + - + +
62C LEU* 3.7 38.5 - - + +
65C HIS* 4.9 3.4 - - + -
66C GLY* 3.9 17.0 - - - +
69C ILE* 4.4 14.6 - - + -
117C VAL* 4.1 20.2 - - + -
121C ILE* 4.4 8.7 - - + -
143C ALA* 6.6 0.2 - - + -
147C LEU* 5.4 2.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 2.9 40.7 + - + +
27C ALA 3.9 3.1 - - - +
29C VAL* 1.3 75.5 - - + +
31C ASP* 1.4 68.2 + - - +
33C ALA* 3.0 10.1 + - + +
34C LEU* 3.0 34.0 + - + +
66C GLY* 5.7 1.6 - - - -
82C GLY* 3.7 36.8 - - - +
87C VAL* 3.8 20.4 - - + -
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA 3.0 17.9 + - - +
28C SER 3.7 3.6 - - - +
30C ILE* 1.4 77.9 - - - +
32C LEU* 1.3 56.7 + - - +
34C LEU* 3.0 14.1 + - - +
35C VAL* 2.9 37.9 + - - +
87C VAL* 4.0 11.8 - - + +
91C THR* 2.6 34.3 + - - +
93C LEU* 3.4 20.3 - - + +
94C LYS 5.2 1.9 - - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER 2.9 17.9 + - - +
29C VAL* 3.6 5.8 - - - +
31C ASP* 1.3 76.2 - - - +
33C ALA* 1.4 57.4 + - - +
35C VAL* 3.3 10.6 + - + +
36C THR* 2.7 33.7 + - - -
62C LEU* 3.8 20.6 - - + -
93C LEU* 3.9 7.8 - - + +
113C ARG* 3.7 31.4 - - + +
114C TYR* 3.6 51.4 - - + -
117C VAL* 4.0 22.0 - - + -
147C LEU* 4.1 3.1 - - + -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 2.9 14.0 + - + +
30C ILE* 3.0 13.9 + - + +
32C LEU* 1.4 75.3 - - - +
34C LEU* 1.3 64.3 + - + +
36C THR* 3.3 8.5 + - - -
37C LYS 3.4 6.2 + - - -
59C ARG* 3.0 45.7 + - - +
62C LEU* 3.7 22.6 - - + +
63C ASP* 4.3 4.5 - - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.0 30.8 + - + +
31C ASP* 3.5 12.8 - - - +
33C ALA* 1.3 76.3 - - + +
35C VAL* 1.3 61.0 + - + +
37C LYS* 3.4 4.7 + - - +
38C GLN* 2.9 27.5 + - - +
41C TRP* 5.3 1.2 - - - -
59C ARG* 4.2 19.1 - - - +
84C LEU* 5.5 11.4 - - + -
87C VAL* 5.6 4.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 2.9 30.6 + - - +
32C LEU* 3.4 21.1 - - + +
34C LEU* 1.3 74.1 - - + +
36C THR* 1.3 59.0 + - - +
38C GLN* 3.2 8.6 + - - +
39C ALA* 2.9 29.8 + - - +
93C LEU* 4.9 0.9 - - + -
94C LYS 5.8 0.4 - - - +
96C TYR* 3.7 37.4 - - + -
110C LEU* 3.5 23.1 - - + -
113C ARG* 4.2 16.8 - - + -
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Residues in contact with THR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU 2.7 21.2 + - - -
33C ALA* 3.5 8.5 - - - -
34C LEU 3.2 0.4 - - - -
35C VAL* 1.3 78.0 - - - +
37C LYS* 1.3 57.3 + - - +
39C ALA* 3.5 2.8 + - - +
40C HIS* 3.0 27.6 + - - +
55C LEU* 3.2 41.1 - - + +
58C PHE* 4.1 1.1 - - + -
59C ARG* 4.0 12.6 - - + +
62C LEU* 3.7 2.6 - - - +
110C LEU* 4.3 6.7 - - - -
114C TYR* 2.7 34.7 + - - +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA 3.4 1.2 + - - -
34C LEU* 3.4 7.6 + - - +
35C VAL 3.3 0.4 - - - -
36C THR* 1.3 76.8 - - - +
38C GLN* 1.4 64.5 + - - +
40C HIS* 3.4 25.0 + - + +
41C TRP* 2.9 62.1 + - + +
56C ASP* 2.7 32.0 + - - +
59C ARG* 3.5 45.5 - - + +
----------------------------------------------------------
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU 2.9 15.7 + - - +
35C VAL* 3.4 12.8 - - - +
37C LYS* 1.4 75.7 - - - +
39C ALA* 1.3 61.4 + - - +
41C TRP* 3.7 18.3 + - - -
42C ASN* 3.0 51.4 + - - +
96C TYR* 3.7 26.9 - - + -
97C PRO 4.9 0.6 - - - +
98C THR* 4.0 29.7 - - + +
106C HIS* 4.5 1.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL 2.9 14.3 + - - +
36C THR 3.8 3.8 - - - +
38C GLN* 1.3 73.8 - - - +
40C HIS* 1.3 67.2 + - - +
42C ASN 3.1 0.9 + - - -
43C LEU* 3.0 29.7 + - - +
55C LEU* 4.0 5.6 - - + -
96C TYR* 3.5 22.2 - - - +
106C HIS* 3.5 18.2 - - + +
110C LEU* 3.8 23.1 - - + -
----------------------------------------------------------
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Residues in contact with HIS 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR 3.0 18.9 + - - +
37C LYS* 3.4 18.8 + - + +
39C ALA* 1.3 76.1 - - - +
41C TRP* 1.4 90.9 + + - +
43C LEU* 3.1 14.6 - - - +
52C HIS* 2.8 79.3 + + - +
55C LEU* 3.7 18.3 - - + +
56C ASP* 3.0 39.3 + - - -
----------------------------------------------------------
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Residues in contact with TRP 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU 5.3 1.1 - - - -
37C LYS* 2.9 57.3 + - + +
38C GLN* 3.8 22.2 - - - -
40C HIS* 1.4 100.6 + + - +
42C ASN* 1.3 71.8 + - - +
43C LEU* 3.6 3.2 + - - +
44C LYS* 4.9 4.3 + - - -
48C PHE* 5.2 3.6 - - - -
52C HIS* 4.8 5.4 - + - -
----------------------------------------------------------
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Residues in contact with ASN 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.0 48.0 + - - +
39C ALA 3.1 2.2 + - - -
41C TRP* 1.3 87.7 - - - +
43C LEU* 1.3 65.5 + - - +
44C LYS* 3.6 13.2 + - - +
98C THR 5.9 2.0 - - - -
100C ILE 4.4 5.2 - - - +
101C TYR* 3.6 34.5 - - + -
106C HIS* 3.9 14.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA 3.0 19.1 + - - +
40C HIS* 3.1 23.3 - - - +
41C TRP 4.6 0.9 - - - +
42C ASN* 1.3 77.5 - - - +
44C LYS* 1.4 66.6 + - - +
48C PHE* 3.3 35.7 - - + +
51C VAL* 3.5 39.7 - - + -
52C HIS* 3.9 12.1 - - + +
55C LEU* 4.7 2.9 - - + -
101C TYR 3.4 5.6 - - - +
103C ILE* 4.1 19.3 - - + -
106C HIS* 3.7 20.6 - - + -
----------------------------------------------------------
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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