Contacts of the helix formed by residues 38 - 64 (chain V) in PDB entry 1BFR
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 LYS 38 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ARG* 5.2 8.9 - - - +
157E GLU* 3.0 29.6 + - - +
33V LYS* 5.5 6.5 - - + +
36V GLY* 3.0 17.1 + - - +
37V LEU* 1.3 70.1 - - - +
39V ARG* 1.3 62.7 + - - +
41V ASN* 3.1 9.5 + - - +
42V ASP* 3.0 29.2 + - - +
153V GLN 3.1 6.1 + - - +
154V ILE 3.0 24.2 + - - +
156V GLU* 3.6 33.2 - - - +
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Residues in contact with ARG 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q LYS* 5.1 9.3 - - - +
154Q ILE* 5.8 8.7 + - - +
155Q ARG* 3.2 26.5 - - - +
38V LYS* 1.3 71.7 - - - +
40V LEU* 1.3 71.0 + - - +
42V ASP* 3.2 4.2 + - - +
43V VAL* 3.1 33.8 + - + +
133V TRP* 3.9 13.7 - - - +
137V GLU* 3.1 40.0 + - - -
152V ALA* 4.0 1.6 - - - -
153V GLN* 2.6 55.5 + - - +
155V ARG 3.7 12.2 + - - +
156V GLU* 4.5 7.9 - - - +
157V GLU* 4.2 23.8 - - + +
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Residues in contact with LEU 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32V PHE* 3.7 38.4 - - + -
37V LEU* 3.1 15.7 + - + +
39V ARG* 1.3 86.2 - - - +
41V ASN* 1.3 64.4 + - - +
43V VAL* 4.4 1.7 - - - +
44V GLU* 3.0 29.6 + - - +
83V VAL* 4.2 11.7 - - + -
87V LEU* 5.0 3.6 - - + -
133V TRP* 4.1 20.2 - - + -
149V TYR* 3.6 28.5 - - + +
150V LEU* 5.7 0.2 - - + -
153V GLN* 3.5 38.5 + - + +
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Residues in contact with ASN 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V ALA* 3.1 33.1 - - - +
30V ARG* 2.9 28.0 + - - +
32V PHE* 3.7 1.6 - - - +
33V LYS* 3.4 37.6 - - + +
37V LEU 3.0 8.8 + - - +
38V LYS* 3.4 10.0 - - - +
40V LEU* 1.3 75.7 - - - +
42V ASP* 1.3 74.9 + - - +
45V TYR* 2.9 26.0 + - - +
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Residues in contact with ASP 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V LYS* 3.0 14.7 + - - +
39V ARG* 3.2 4.9 + - - +
41V ASN* 1.3 92.3 + - - +
43V VAL* 1.3 61.9 + - + +
45V TYR* 3.8 3.2 - - - +
46V HIS* 2.7 44.7 + - + +
156V GLU* 3.3 38.6 - - - +
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Residues in contact with VAL 43 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39V ARG* 3.1 27.8 + - + +
40V LEU 4.4 0.7 - - - +
42V ASP* 1.3 75.4 - - + +
44V GLU* 1.3 62.1 + - - +
46V HIS* 3.2 8.4 + - + +
47V GLU* 3.0 30.1 + - + +
133V TRP* 3.5 55.0 - - + +
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Residues in contact with GLU 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR* 3.5 25.6 - - - +
28V HIS* 3.3 19.8 - - - +
29V ALA* 3.9 18.6 - - + +
32V PHE* 3.8 17.1 - - + -
40V LEU 3.0 19.9 + - - +
43V VAL* 1.3 73.6 - - - +
45V TYR* 1.3 63.2 + - - +
47V GLU* 3.1 7.6 + - - +
48V SER* 2.9 21.5 + - - -
87V LEU* 4.4 2.4 - - - +
90V ASP* 2.8 28.2 - - - +
133V TRP* 3.5 27.8 - - + -
134V LEU* 4.1 3.1 - - - +
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Residues in contact with TYR 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V PHE* 3.6 33.0 - + - -
29V ALA* 3.5 11.2 - - + +
30V ARG* 3.7 28.9 - - - +
41V ASN* 2.9 21.0 + - - +
42V ASP* 3.8 3.6 - - - +
44V GLU* 1.3 75.3 - - - +
46V HIS* 1.3 84.4 + + - +
48V SER* 3.1 8.4 - - - -
49V ILE* 3.0 43.9 + - + +
200V HEM 3.6 30.0 + - + +
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Residues in contact with HIS 46 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42V ASP* 2.7 35.4 + - + +
43V VAL* 3.2 9.5 + - + +
45V TYR* 1.3 96.0 - + - +
47V GLU* 1.3 64.3 + - + +
49V ILE* 3.1 11.2 + - + +
50V ASP* 2.9 27.3 + - - +
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Residues in contact with GLU 47 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR* 3.2 39.3 + - + -
43V VAL* 3.0 20.9 + - + +
44V GLU* 3.1 9.9 + - - +
46V HIS* 1.3 74.6 - - + +
48V SER* 1.3 64.3 + - - +
50V ASP* 3.2 5.7 + - - +
51V GLU* 3.0 28.6 + - - +
130V HIS* 3.5 44.2 - - + +
133V TRP* 3.8 31.9 - - - +
134V LEU* 4.6 1.2 - - - +
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Residues in contact with SER 48 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V ILE* 3.2 21.3 + - - +
25V TYR* 3.9 9.0 - - - +
26V PHE* 3.4 28.0 - - - -
44V GLU 2.9 12.5 + - - -
45V TYR* 3.1 11.9 - - - -
47V GLU* 1.3 75.0 - - - +
49V ILE* 1.3 61.9 + - - +
51V GLU* 3.1 7.8 + - - +
52V MET* 3.0 41.3 + - - +
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Residues in contact with ILE 49 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V TYR* 3.0 55.4 + - + +
46V HIS* 3.6 11.9 - - + +
48V SER* 1.3 73.8 - - - +
50V ASP* 1.3 62.4 + - - +
52V MET* 3.2 26.3 - - + +
53V LYS* 2.9 31.8 + - - +
200V HEM 3.8 51.8 - - + +
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Residues in contact with ASP 50 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V HIS* 2.9 23.1 + - - +
47V GLU* 3.5 9.1 - - - +
49V ILE* 1.3 71.4 - - - +
51V GLU* 1.3 60.0 + - - +
53V LYS* 3.4 17.1 + - - +
54V HIS* 2.8 42.2 + - + +
126V ASP* 5.1 6.9 - - - +
130V HIS* 2.8 33.5 + - + -
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Residues in contact with GLU 51 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V GLU* 2.8 11.8 - - - +
21V ALA* 3.9 16.3 - - + +
22V ILE* 3.6 23.5 - - + +
25V TYR* 3.6 9.9 - - + -
47V GLU 3.0 14.5 + - - +
48V SER 3.6 3.1 - - - +
50V ASP* 1.3 71.1 - - - +
52V MET* 1.3 61.1 + - - +
54V HIS* 2.8 16.0 + - - +
55V ALA* 2.8 31.0 + - - +
94V GLU* 3.2 7.1 - - - +
127V GLU* 2.9 2.6 - - - +
130V HIS* 3.4 5.4 + - - -
201V MN 2.0 33.7 + - - -
202V MN 2.0 34.7 + - - -
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Residues in contact with MET 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V ILE* 3.6 23.3 - - + +
26V PHE* 4.1 4.0 - - + -
48V SER* 3.0 33.5 + - - +
49V ILE* 3.2 24.0 - - + +
51V GLU* 1.3 75.6 - - - +
53V LYS* 1.3 58.0 + - - +
55V ALA* 3.2 3.3 + - - +
56V ASP* 2.9 27.4 + - - +
200V HEM 2.2 100.8 - - + +
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Residues in contact with LYS 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49V ILE* 2.9 25.8 + - - +
50V ASP* 3.6 18.1 + - - +
52V MET* 1.3 73.8 - - - +
54V HIS* 1.3 64.0 + - + +
56V ASP* 3.4 9.6 + - - +
57V ARG* 3.1 26.4 + - + +
200V HEM 3.5 43.3 - - + -
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Residues in contact with HIS 54 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V GLU* 3.6 15.0 - - + +
50V ASP* 2.8 28.5 + - + +
51V GLU* 2.8 12.9 + - - +
53V LYS* 1.3 73.1 - - + +
55V ALA* 1.3 62.8 + - - +
57V ARG* 3.0 23.5 + - - +
58V TYR* 3.1 18.3 + - + -
123V ILE* 3.6 29.9 - - + +
126V ASP* 2.8 38.3 + - + -
127V GLU* 3.1 18.2 - - - -
130V HIS* 4.9 0.4 - + - -
202V MN 2.5 23.8 + - - -
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Residues in contact with ALA 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V LEU* 3.8 22.8 - - + +
18V GLU* 4.2 7.7 - - + +
19V LEU* 4.6 2.9 - - + -
22V ILE* 4.0 13.7 - - + -
51V GLU 2.8 15.0 + - - +
52V MET 3.4 8.5 - - - +
54V HIS* 1.3 70.0 - - - +
56V ASP* 1.3 58.5 + - - +
58V TYR* 3.2 8.0 + - - +
59V ILE* 2.9 34.9 + - - +
200V HEM 4.0 15.7 - - + -
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Residues in contact with ASP 56 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U PHE* 3.4 24.3 - - + -
30U ARG* 2.9 44.8 + - - +
52V MET 2.9 12.2 + - - +
53V LYS* 3.5 13.0 - - - +
54V HIS 3.2 0.2 - - - -
55V ALA* 1.3 76.5 - - - +
57V ARG* 1.3 61.4 + - - +
59V ILE* 3.5 1.9 + - - +
60V GLU* 3.0 35.7 + - - +
200V HEM 4.3 9.6 - - + +
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Residues in contact with ARG 57 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V LYS* 3.1 14.3 + - - +
54V HIS* 3.0 16.0 + - - +
56V ASP* 1.3 74.9 - - + +
58V TYR* 1.3 62.6 + - - +
60V GLU* 3.4 5.1 + - - +
61V ARG* 3.0 24.3 + - - +
119V MET* 3.6 39.9 - - + +
122V GLU* 3.0 47.8 + - - +
123V ILE* 4.1 18.2 - - + +
126V ASP* 5.8 1.4 + - - -
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Residues in contact with TYR 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V LEU* 4.2 21.3 - - + +
14V LEU* 3.8 31.4 - - + +
15V LEU* 4.0 26.9 - - + -
18V GLU* 3.7 27.4 + - + -
54V HIS 3.1 22.1 + - - -
55V ALA* 3.7 4.5 - - - +
57V ARG* 1.3 72.7 - - - +
59V ILE* 1.4 58.7 + - - +
61V ARG* 3.1 5.0 + - - +
62V ILE* 2.9 38.4 + - + +
101V LEU* 3.7 23.2 - - - +
119V MET* 3.5 27.8 - - + -
120V MET* 4.4 3.1 - - + -
123V ILE* 3.5 27.8 - - + +
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Residues in contact with ILE 59 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U PHE* 3.8 28.0 - - + -
27U LEU* 4.0 9.0 - - + +
30U ARG* 3.9 17.5 - - + -
15V LEU* 4.0 19.0 - - + +
55V ALA* 2.9 25.4 + - + +
56V ASP* 3.8 4.7 - - - +
58V TYR* 1.4 72.3 - - - +
60V GLU* 1.3 62.8 + - - +
62V ILE* 4.8 0.7 - - - -
63V LEU* 3.1 41.0 + - + +
69V PRO* 3.8 19.2 - - + +
71V LEU* 3.9 26.0 - - + -
200V HEM 4.4 5.6 - - + -
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U ARG* 3.2 26.0 + - + +
33U LYS* 3.4 30.6 + - - -
56V ASP* 3.0 41.2 + - - +
57V ARG* 3.9 5.4 - - - +
59V ILE* 1.3 77.2 - - - +
61V ARG* 1.3 60.9 + - - +
63V LEU* 3.5 6.5 + - + +
64V PHE* 3.1 22.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 61 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S GLU* 2.9 31.1 + - - +
1V MET* 5.0 0.6 - - - +
11V LEU* 3.9 20.9 - - + -
57V ARG 3.0 18.4 + - - +
58V TYR 3.8 2.7 - - - +
60V GLU* 1.3 74.4 - - - +
62V ILE* 1.3 63.7 + - - +
64V PHE* 3.2 27.1 + - - +
65V LEU* 2.9 42.3 + - + +
113V ASP* 3.1 24.9 + - - -
115V VAL* 3.7 16.6 - - - +
116V SER* 3.0 22.0 + - - +
119V MET* 4.0 24.2 - - + -
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Residues in contact with ILE 62 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ILE* 4.0 13.0 - - + +
11V LEU* 3.7 27.4 - - + +
12V ASN* 3.6 38.8 - - - +
15V LEU* 4.2 11.2 - - + -
58V TYR 2.9 29.5 + - - +
59V ILE 4.0 3.1 - - - +
61V ARG* 1.3 70.5 - - - +
63V LEU* 1.3 61.4 + - - +
65V LEU* 3.3 6.6 + - - +
66V GLU 3.2 4.7 + - - -
67V GLY* 2.9 50.8 + - - -
68V LEU 3.7 15.0 - - - +
69V PRO* 3.7 5.2 - - + -
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Residues in contact with LEU 63 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U LEU* 4.5 1.1 - - + -
30U ARG* 3.9 30.3 - - + +
31U MET* 4.1 20.2 - - + +
34U ASN* 3.9 29.3 + - + +
59V ILE* 3.1 42.1 + - + +
60V GLU* 3.7 5.8 - - - +
62V ILE* 1.3 76.3 - - - +
64V PHE* 1.3 61.7 + - - +
66V GLU* 3.0 17.0 + - - +
67V GLY 4.0 7.9 - - - +
68V LEU* 5.1 2.2 - - + -
69V PRO* 3.4 27.1 - - + -
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Residues in contact with PHE 64 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S GLU* 3.6 24.0 - - + -
131S ILE* 4.7 0.9 - - + -
132S ASP* 3.5 47.8 - - + +
135S GLU* 4.1 4.5 - - - -
34U ASN* 4.2 10.1 + - - +
1V MET* 2.9 77.3 + - + +
60V GLU 3.1 14.1 + - - +
61V ARG* 3.2 37.9 + - - +
63V LEU* 1.3 74.0 - - - +
65V LEU* 1.3 62.8 + - + +
66V GLU* 3.0 4.0 + - - +
----------------------------------------------------------
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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