Contacts of the helix formed by residues 10 - 41 (chain C) in PDB entry 1VEQ
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 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLY 4.3 0.4 + - - -
9C LEU* 1.3 73.2 - - - +
11C ASP* 1.3 54.2 + - - +
12C LYS* 2.6 21.4 + - - +
13C LYS* 2.9 53.0 + - - +
14C ALA* 2.9 10.8 + - - +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C SER 4.8 8.8 - - - +
4C PHE 5.0 1.6 - - - +
5C THR* 3.9 25.0 - - - +
9C LEU 3.3 2.4 + - - +
10C SER* 1.3 69.0 - - - +
12C LYS* 1.3 58.4 + - - +
14C ALA* 4.2 9.0 - - - +
15C SER* 3.6 20.4 + - - -
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Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 2.6 12.6 + - - +
11C ASP* 1.3 73.1 - - - +
13C LYS* 1.3 76.3 + - + +
14C ALA 3.1 0.9 - - - -
15C SER* 3.1 5.7 + - - -
16C ASP* 2.6 53.6 + - - +
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Residues in contact with LYS 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.6 13.9 - - + -
10C SER* 2.9 31.1 + - - +
12C LYS* 1.3 86.7 - - + +
14C ALA* 1.3 63.6 + - - +
16C ASP* 3.0 7.8 + - - +
17C VAL* 3.0 27.8 + - - +
129C ASP 4.1 16.9 + - - +
130C LEU* 4.4 31.3 + - + +
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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
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5C THR* 3.6 23.8 - - - +
9C LEU* 4.2 22.8 - - + +
10C SER 2.9 15.0 + - - +
11C ASP* 4.2 7.2 - - - +
13C LYS* 1.3 77.2 - - - +
15C SER* 1.3 61.7 + - - +
17C VAL* 3.1 7.5 + - - +
18C ALA* 3.1 21.0 + - - +
75C LEU* 3.8 17.6 - - + +
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Residues in contact with SER 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP 3.6 16.7 + - - -
12C LYS* 3.1 7.4 + - - -
14C ALA* 1.3 80.1 - - - +
16C ASP* 1.3 63.3 + - - +
18C ALA* 3.5 8.2 - - - +
19C ASP* 3.1 30.9 + - - +
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 2.6 47.6 + - - +
13C LYS* 3.0 10.7 + - - +
15C SER* 1.3 76.7 - - - +
17C VAL* 1.3 66.0 + - - +
19C ASP* 3.7 11.7 + - - +
20C LEU* 3.3 23.4 + - - +
130C LEU* 4.5 16.2 - - + +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 5.3 2.2 - - + -
13C LYS 3.0 16.9 + - - +
14C ALA* 3.1 9.2 + - - +
16C ASP* 1.3 74.5 - - - +
18C ALA* 1.3 68.3 + - - +
20C LEU* 2.8 18.6 + - - +
21C LEU* 3.0 18.6 + - + +
75C LEU* 3.7 17.9 - - + -
127C LEU* 4.0 15.3 - - + -
130C LEU* 3.7 32.5 - - + -
131C ASP* 4.3 11.9 - - + -
134C SER* 3.9 20.0 - - - +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ALA 3.1 9.7 + - - +
15C SER* 3.5 13.2 - - - +
17C VAL* 1.3 78.5 - - - +
19C ASP* 1.3 65.0 + - - +
20C LEU 2.9 0.9 + - - -
21C LEU* 2.9 7.5 + - - +
22C GLN* 2.8 25.6 + - - +
72C ILE* 4.5 10.5 - - + +
75C LEU* 3.9 14.3 - - + +
77C LYS* 3.8 29.2 - - + -
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Residues in contact with ASP 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.1 21.0 + - - +
16C ASP* 3.7 16.2 - - - +
18C ALA* 1.3 79.5 - - - +
20C LEU* 1.3 61.2 + - - +
22C GLN* 3.7 8.7 + - - +
23C LYS* 3.5 17.8 + - - +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ASP 3.3 13.0 + - - +
17C VAL* 2.8 12.2 + - - +
19C ASP* 1.3 77.1 - - + +
21C LEU* 1.3 69.6 + - + +
23C LYS* 3.3 15.5 + - + +
24C GLN* 3.2 17.0 + - - +
123C SER* 3.4 36.4 + - - +
126C LYS* 4.5 26.5 - - + +
127C LEU* 4.1 30.5 - - + -
130C LEU* 4.2 11.7 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 3.4 30.3 - - + +
18C ALA* 2.9 2.6 + - - +
20C LEU* 1.3 75.0 - - + +
22C GLN* 1.3 61.5 + - - +
23C LYS 2.8 1.8 - - - -
24C GLN* 2.6 29.0 + - + +
25C LEU* 2.7 13.5 + - - +
68C VAL* 3.6 17.9 - - + +
71C ARG* 3.8 30.3 - - + -
72C ILE* 3.7 19.7 - - + -
75C LEU* 4.5 5.4 - - + -
127C LEU* 4.9 8.7 - - + -
134C SER* 4.5 6.3 - - - +
137C LEU* 6.0 0.4 - - + -
138C LEU* 4.1 27.8 - - + -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA 2.8 15.9 + - - +
19C ASP* 3.8 11.7 - - - +
21C LEU* 1.3 76.6 - - - +
23C LYS* 1.3 60.9 + - - +
25C LEU* 3.7 5.6 + - - +
26C SER* 3.4 17.7 + - - -
72C ILE* 3.5 13.7 - - + +
78C SER 4.3 2.1 - - - +
79C PRO* 3.6 9.7 - - - +
80C LYS* 3.0 53.0 + - + +
85C ALA* 4.9 0.2 - - - +
89C ASP* 3.2 26.6 + - - +
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASP 3.5 8.7 + - - +
20C LEU* 3.3 18.1 + - + +
21C LEU 2.7 1.4 + - - -
22C GLN* 1.3 76.9 - - - +
24C GLN* 1.3 67.3 + - - +
26C SER* 3.2 4.9 + - - -
27C THR* 2.9 30.1 + - - +
89C ASP* 4.7 26.9 - - + +
91C THR* 5.2 14.9 + - - +
119C ASP* 3.4 28.1 + - + +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU 3.2 4.7 + - - +
21C LEU* 2.6 24.2 + - + +
23C LYS* 1.3 76.6 - - - +
25C LEU* 1.3 58.2 + - - +
27C THR* 2.9 14.9 + - - +
28C TYR* 2.8 60.9 + - + +
68C VAL* 4.8 4.3 - - + -
116C VAL* 5.4 0.8 - - - +
119C ASP* 4.6 6.1 - - - +
120C THR* 2.6 35.3 + - - -
123C SER* 4.3 14.4 + - - -
138C LEU* 3.1 32.0 - - + +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU 2.7 16.8 + - - +
22C GLN* 3.7 11.0 - - - +
24C GLN* 1.3 73.0 - - - +
26C SER* 1.3 66.9 + - - +
28C TYR* 3.1 13.4 + - - +
29C ASN* 2.9 54.4 + - - +
65C ALA* 4.3 8.3 - - - +
68C VAL* 4.3 8.0 - - + +
69C ALA* 3.2 44.6 - - + +
72C ILE* 4.5 6.7 - - + -
79C PRO* 4.6 5.4 - - + -
80C LYS 3.4 26.0 - - - +
81C GLY* 4.3 2.0 - - - -
40I TRP* 4.4 9.6 - - + -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.4 11.4 + - - -
23C LYS 3.2 8.1 + - - -
25C LEU* 1.3 81.6 - - - +
27C THR* 1.3 63.1 + - - +
29C ASN* 3.3 10.9 + - - +
30C ASP* 3.0 22.9 + - - +
80C LYS 4.4 0.9 + - - -
85C ALA 3.9 0.5 + - - -
86C ILE* 3.7 28.5 + - - +
89C ASP* 3.1 38.2 + - - +
90C ARG* 5.0 4.9 - - - +
92C TRP* 5.3 0.4 - - - -
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 2.9 23.2 + - - +
24C GLN* 2.9 21.2 + - - +
26C SER* 1.3 79.5 - - - +
28C TYR* 1.3 63.3 + - + +
30C ASP* 3.3 3.5 + - - +
31C LEU* 3.0 20.1 + - - +
90C ARG* 6.2 0.4 - - - -
92C TRP* 3.4 36.6 - - + -
115C GLY 5.6 0.2 - - - +
116C VAL* 4.0 32.1 - - + +
119C ASP* 5.2 9.4 + - + +
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 2.8 51.1 + - + +
25C LEU* 3.1 6.9 + - - +
27C THR* 1.3 77.8 - - + +
29C ASN* 1.3 59.3 + - - +
31C LEU* 2.9 12.9 + - + +
32C HIS* 2.7 36.5 + - - +
61C VAL* 3.8 22.0 - - + +
64C TYR* 3.6 36.1 - + + -
65C ALA* 4.3 8.1 - - + -
68C VAL* 3.7 19.1 - - + -
116C VAL* 4.7 9.4 - - + -
120C THR* 4.7 1.0 + - - +
138C LEU* 3.9 2.4 - - - +
141C HIS* 2.7 32.4 + + + +
145C LEU* 4.6 15.0 - - + +
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 2.9 50.3 + - - +
26C SER* 3.7 6.7 - - - +
28C TYR* 1.3 76.7 - - - +
30C ASP* 1.3 64.6 + - - +
32C HIS* 3.5 21.5 + - - +
33C LEU* 3.1 27.9 + - - +
65C ALA* 4.2 12.2 - - - +
81C GLY* 4.4 11.5 - - - -
86C ILE* 4.0 16.7 - - + +
33I LEU* 3.7 23.4 - - + +
40I TRP* 5.0 5.1 - - - -
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER 3.0 12.8 + - - +
27C THR 3.5 8.7 - - - +
29C ASN* 1.3 74.6 - - - +
31C LEU* 1.3 56.7 + - - +
33C LEU* 3.0 4.0 + - - +
34C THR* 2.7 46.1 + - - +
86C ILE* 3.5 13.8 - - + +
90C ARG* 3.2 12.2 + - + -
92C TRP* 3.4 32.3 + - + +
94C ASP* 4.4 4.0 - - - +
95C TYR 5.6 0.5 + - - -
112C VAL* 5.0 9.5 - - - +
83I PRO* 2.8 31.7 - - - +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR 3.0 11.4 + - - +
28C TYR* 2.9 12.3 + - + +
30C ASP* 1.3 80.8 + - - +
32C HIS* 1.3 52.0 + - - +
34C THR* 2.9 9.1 + - - -
35C LEU* 2.7 59.6 + - + +
61C VAL* 3.6 30.1 - - + -
109C LEU* 5.7 0.9 - - + -
112C VAL* 4.6 11.0 - - + -
113C TYR* 3.3 29.2 - - + +
116C VAL* 4.5 26.0 - - + -
145C LEU* 4.0 16.2 - - + -
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Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR 2.7 13.8 + - - -
29C ASN* 3.5 39.7 + - - +
31C LEU* 1.3 75.0 - - - +
33C LEU* 1.3 80.4 + - + +
35C LEU* 3.7 11.5 - - - +
36C LYS* 3.3 21.1 + - - +
58C VAL* 4.2 7.2 - - + +
61C VAL* 3.5 24.5 - - + -
62C ARG* 4.2 24.4 + - + +
65C ALA* 5.1 2.6 - - + +
32I HIS* 4.3 19.5 - + - -
33I LEU* 4.5 5.8 - - + +
62I ARG* 3.3 26.4 + - - +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN 3.1 18.0 + - - +
30C ASP* 3.0 4.9 + - - +
32C HIS* 1.3 97.7 + - + +
34C THR* 1.3 58.3 + - - +
36C LYS* 3.5 8.8 + - + +
37C HIS* 3.1 19.2 + - - +
40C TRP* 5.0 3.4 - - + -
86C ILE* 5.1 1.8 - - + -
29I ASN* 3.7 29.8 - - + +
32I HIS* 4.6 6.1 - - - +
33I LEU* 3.7 27.4 - - + -
81I GLY 3.3 31.6 - - - +
82I THR 5.0 0.4 - - - -
83I PRO* 4.6 22.4 - - + -
86I ILE* 5.2 5.6 - - + -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASP* 2.7 36.3 + - - -
31C LEU* 3.3 10.8 - - - -
33C LEU* 1.3 75.5 - - - +
35C LEU* 1.3 58.1 + - - +
37C HIS* 2.8 32.3 + - + +
38C VAL* 3.0 13.4 + - + +
95C TYR* 3.5 45.9 + - + +
109C LEU* 4.7 8.1 - - + -
112C VAL* 5.3 8.3 - - + -
82I THR* 4.5 5.2 - - - +
83I PRO* 4.2 5.9 - - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 2.7 66.4 + - + +
32C HIS* 3.7 6.1 - - - +
34C THR* 1.3 71.8 - - - +
36C LYS* 1.3 58.1 + - - +
38C VAL* 3.1 11.6 + - - +
39C HIS* 2.9 25.3 + - - +
54C ILE* 3.5 23.5 - - + +
57C GLN* 4.5 5.6 - - + +
58C VAL* 3.3 24.0 - - + -
61C VAL* 5.1 0.9 - - + -
109C LEU* 4.0 27.4 - - + -
113C TYR* 3.5 16.6 - - + +
148C PHE* 4.1 8.5 - - + -
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS 3.3 9.6 + - - +
33C LEU* 3.7 12.3 - - + +
34C THR 3.2 0.4 - - - -
35C LEU* 1.3 80.0 - - - +
37C HIS* 1.3 62.8 + - - +
39C HIS* 3.0 32.1 + - + +
40C TRP* 3.1 48.2 + - + -
55C ASP* 3.1 20.3 + - - +
58C VAL* 3.7 26.9 - - + -
62I ARG* 4.7 19.7 - - + +
65I ALA* 6.1 1.3 - - + -
66I ASP* 2.9 39.5 + - - +
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Residues in contact with HIS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 3.1 11.0 + - - +
34C THR* 2.8 22.2 + - - +
36C LYS* 1.3 77.5 - - - +
38C VAL* 1.3 57.6 + - - -
40C TRP* 3.2 18.4 + - - +
41C ASN* 2.7 45.6 + - - -
95C TYR* 3.5 29.9 + + - -
97C VAL 3.1 18.6 + - - -
98C GLU* 4.8 3.5 + - - -
105C HIS* 5.4 0.2 - + - -
79I PRO 3.4 14.5 + - - -
80I LYS* 3.4 12.9 - - + +
81I GLY* 2.9 28.7 + - - +
82I THR* 3.9 17.9 - - + +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C THR 3.0 17.7 + - - +
35C LEU* 3.6 4.7 - - - +
37C HIS* 1.3 69.9 - - - +
39C HIS* 1.3 64.9 + - - +
40C TRP 2.7 6.8 + - - -
41C ASN 3.2 7.1 + - - +
42C VAL* 2.7 34.4 - - + +
50C VAL* 5.4 0.9 - - + -
54C ILE* 3.1 26.7 - - + -
95C TYR* 3.8 25.6 - - + +
105C HIS* 4.0 27.1 - - + +
106C LEU* 6.5 0.9 - - + -
109C LEU* 4.2 21.8 - - + -
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU 2.9 14.0 + - - +
36C LYS* 3.0 40.1 + - + +
38C VAL* 1.3 76.7 - - - +
40C TRP* 1.3 64.2 + + - +
42C VAL* 4.8 1.9 + - - +
47C PHE* 5.0 1.4 - - - -
51C HIS* 2.7 85.7 + + - +
52C GLU* 5.1 0.7 - - - -
54C ILE* 3.9 20.2 - - + +
55C ASP* 3.3 19.8 - - - -
150H TRP* 5.0 0.5 - - - -
66I ASP* 3.1 7.6 + - - -
70I GLU* 3.2 2.2 + - - -
203I FE 2.2 27.3 - - - -
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Residues in contact with TRP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.0 2.7 - - + -
36C LYS* 3.1 47.3 + - + -
37C HIS* 3.5 18.2 - - - +
38C VAL 2.7 2.0 + - - -
39C HIS* 1.3 86.0 - + - +
41C ASN* 1.3 65.0 + - - +
42C VAL 3.4 8.3 + - - +
43C VAL* 5.7 0.7 - - - +
47C PHE* 5.7 0.3 - - - -
150H TRP* 3.7 25.4 - + - -
25I LEU* 4.3 11.2 - - + -
29I ASN* 5.0 6.5 - - - -
65I ALA* 4.0 9.4 - - + -
66I ASP* 3.3 34.4 + - - +
69I ALA* 3.1 32.6 - - + +
70I GLU* 3.6 24.4 - - + +
73I ALA* 4.3 7.1 - - + +
79I PRO* 4.5 15.7 - - + -
81I GLY* 4.2 21.1 - - - -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS* 2.7 58.0 + - - +
38C VAL 3.2 3.2 + - - -
40C TRP* 1.3 76.6 - - - +
42C VAL* 1.3 60.5 + - - +
43C VAL* 4.7 2.5 - - - -
98C GLU* 3.7 6.9 - - - +
99C ARG* 3.3 24.3 - - - +
100C ASP 3.1 23.6 + - - -
105C HIS* 3.1 9.1 + - - +
78I SER* 3.0 20.1 + - - -
79I PRO* 3.0 26.2 + - - +
----------------------------------------------------------
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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