Contacts of the helix formed by residues 40 - 66 (chain C) in PDB entry 2DYS
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 MET 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 3.3 27.6 - - + -
39C SER* 1.3 73.8 + - - +
41C THR* 1.3 58.7 + - - +
42C LEU 3.4 2.2 - - - -
43C LEU* 3.1 12.1 + - + +
44C MET* 2.8 56.1 + - + +
302C DMU 2.8 53.4 - - + +
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Residues in contact with THR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 3.5 14.8 + - - -
40C MET* 1.3 75.7 - - - +
42C LEU* 1.3 63.6 + - - +
44C MET* 3.0 19.3 + - - +
45C ILE* 3.1 29.4 + - + +
45J TYR* 3.3 32.7 + - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.6 39.2 - - + +
29C SER* 3.4 34.8 - - - +
30C GLY* 3.5 10.5 - - - -
33C MET* 4.7 12.3 - - + +
39C SER* 4.9 2.0 + - - -
40C MET 3.4 0.2 - - - -
41C THR* 1.3 80.0 - - - +
43C LEU* 1.3 64.2 + - - +
44C MET 3.1 0.5 + - - -
45C ILE* 3.2 6.8 + - + +
46C GLY 2.9 19.8 + - - -
42J GLY* 3.7 13.9 - - - +
45J TYR* 3.9 22.1 - - + -
46J SER* 4.0 14.6 - - - -
49J CYS* 4.4 14.6 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU 4.3 2.2 - - - -
27C MET* 3.7 28.0 - - + +
30C GLY* 3.4 17.3 + - - +
31C LEU* 3.8 28.3 - - + -
34C TRP* 4.2 21.8 - - + -
40C MET* 3.1 15.7 + - + +
42C LEU* 1.3 78.1 - - - +
44C MET* 1.3 63.7 + - + +
46C GLY* 3.4 0.5 + - - -
47C LEU* 3.0 56.4 + - + +
302C DMU 4.4 24.2 - - + +
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Residues in contact with MET 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 2.8 54.1 + - + +
41C THR* 3.2 10.5 - - - +
43C LEU* 1.3 81.4 - - + +
45C ILE* 1.3 62.0 + - + +
47C LEU* 3.5 22.1 + - + +
48C THR* 2.7 34.2 + - - -
302C DMU 5.6 6.7 - - + +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.8 21.3 - - + -
41C THR* 3.1 32.4 + - + +
42C LEU* 3.6 6.7 - - + +
44C MET* 1.3 74.1 - - + +
46C GLY* 1.3 67.1 + - - +
48C THR* 3.1 7.4 + - - -
49C THR* 3.0 28.3 + - + +
38J LEU* 3.9 28.7 - - + +
42J GLY* 4.4 10.1 - - - +
45J TYR* 4.5 13.2 - - + -
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 3.7 1.5 - - - -
26C LEU* 3.3 26.4 - - - +
27C MET* 3.4 17.5 - - - +
42C LEU 2.9 14.2 + - - -
43C LEU 3.8 0.4 - - - -
45C ILE* 1.3 78.0 - - - +
47C LEU* 1.3 62.2 + - - +
49C THR* 3.0 17.0 + - - -
50C ASN* 3.0 14.0 + - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 3.7 22.8 - - + +
43C LEU* 3.0 38.0 + - + +
44C MET* 3.8 24.7 - - + +
46C GLY* 1.3 74.1 - - - +
48C THR* 1.3 56.4 + - - +
50C ASN* 3.3 3.0 + - - +
51C MET* 3.0 50.1 + - + +
302C DMU 4.9 26.0 - - + -
307C PGV 6.0 0.9 - - + -
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C MET 2.7 19.7 + - - -
45C ILE* 3.4 10.8 - - - -
47C LEU* 1.3 76.0 - - - +
49C THR* 1.3 60.5 + - - +
51C MET* 3.2 8.7 + - - +
52C LEU* 3.0 28.9 + - + +
309C CDL 3.9 28.2 - - + +
38J LEU* 4.1 22.0 - - + -
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 2.9 24.9 - - - -
26C LEU* 4.2 1.4 - - + +
45C ILE* 3.0 17.6 + - + +
46C GLY* 3.0 8.3 + - - -
48C THR* 1.3 71.7 - - - +
50C ASN* 1.3 56.8 + - - +
52C LEU* 3.6 10.0 - - - +
53C THR* 2.7 35.0 + - - -
35J THR* 4.3 3.0 - - - +
38J LEU* 3.4 37.2 - - + -
39J CYS* 3.6 30.3 - - - +
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Residues in contact with ASN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PGV 3.0 34.0 - - - +
20C GLY* 5.2 0.2 - - - -
23C SER* 3.2 16.0 + - - +
27C MET* 3.6 16.4 - - + +
46C GLY 3.0 15.3 + - - +
47C LEU* 3.4 4.7 - - - +
48C THR 3.1 0.2 - - - -
49C THR* 1.3 83.6 + - - +
51C MET* 1.3 63.7 + - - +
53C THR* 3.3 2.3 + - - -
54C MET* 3.0 64.4 + - - +
307C PGV 3.9 15.3 - - - +
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Residues in contact with MET 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.0 42.8 + - + +
48C THR* 3.2 5.1 + - - +
50C ASN* 1.3 81.3 - - - +
52C LEU* 1.3 57.8 + - - +
54C MET* 3.5 25.1 + - + +
55C TYR* 2.9 31.4 + - - +
307C PGV 4.2 15.0 - - + -
309C CDL 3.1 83.8 - - + +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 3.0 23.1 + - + +
49C THR* 3.6 7.9 - - - +
51C MET* 1.3 76.5 - - - +
53C THR* 1.3 61.1 + - - +
55C TYR* 3.7 4.1 - - + +
56C GLN* 3.1 33.7 + - - +
309C CDL 3.7 43.5 - - + -
31J LEU* 4.0 22.4 - - + -
34J VAL* 4.2 7.2 - - + -
35J THR* 3.4 37.7 - - + +
38J LEU* 4.0 21.3 - - + -
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PGV 3.8 16.2 - - + -
16C TRP* 3.4 28.7 - - + +
19C THR* 2.9 31.4 + - - +
20C GLY* 3.6 15.7 - - - -
49C THR 2.7 26.5 + - - -
50C ASN* 3.6 5.8 - - - -
52C LEU* 1.3 73.6 - - - +
54C MET* 1.3 57.7 + - - +
56C GLN* 3.9 4.6 - - - +
57C TRP* 2.9 37.8 + - + +
35J THR* 4.2 1.9 - - - +
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Residues in contact with MET 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PGV 3.7 30.7 - - + -
50C ASN* 3.0 41.2 + - - +
51C MET* 3.6 15.7 - - + +
53C THR* 1.3 75.2 - - - +
55C TYR* 1.3 63.5 + - - +
57C TRP* 3.9 0.2 - - - +
58C TRP* 3.0 63.2 + - + +
307C PGV 3.6 50.3 - - + -
309C CDL 3.6 15.7 - - + -
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C MET 2.9 19.9 + - - +
52C LEU* 3.7 2.5 - - - +
54C MET* 1.3 76.5 - - - +
56C GLN* 1.3 67.8 + - + +
59C ARG* 2.9 40.6 + - - +
309C CDL 3.1 171.1 + - + +
31J LEU* 4.0 13.7 - - + -
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Residues in contact with GLN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 3.0 48.4 - - + +
52C LEU* 3.1 26.1 + - - +
53C THR 4.1 1.1 - - - +
55C TYR* 1.3 86.9 - - + +
57C TRP* 1.3 60.5 + - - +
59C ARG* 3.2 24.1 + - - +
60C ASP* 3.0 33.4 + - - +
28J ASP 4.6 1.2 - - - +
31J LEU* 3.6 27.4 - - + +
32J TYR* 3.8 4.7 + - - +
35J THR* 2.9 27.3 + - - -
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Residues in contact with TRP 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.6 14.8 - - + +
97A MET* 3.9 22.7 - - - -
100A MET* 3.7 38.8 - - + -
607A PGV 2.8 80.4 + - + -
16C TRP* 3.6 35.8 - + + -
17C PRO* 3.9 21.1 - - + -
53C THR* 2.9 20.9 + - + +
54C MET 3.9 2.7 - - - +
56C GLN* 1.3 77.8 - - - +
58C TRP* 1.3 65.7 + + - +
60C ASP* 3.3 4.2 + - - +
61C VAL* 3.1 27.1 + - + +
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Residues in contact with TRP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PGV 2.8 46.4 + - + +
54C MET* 3.0 57.8 + - + +
57C TRP* 1.3 81.0 - + - +
59C ARG* 1.3 64.5 + - - +
61C VAL* 3.1 10.3 + - + +
62C ILE* 3.0 25.6 + - - +
307C PGV 3.6 107.7 - - + +
309C CDL 3.7 27.1 - - + -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 4.0 11.7 - - - -
55C TYR* 2.9 29.3 + - + +
56C GLN* 3.2 25.8 + - - +
58C TRP* 1.3 73.4 - - - +
60C ASP* 1.3 84.8 + - - +
62C ILE* 2.9 10.1 + - - +
63C ARG* 2.9 47.3 + - - +
309C CDL 3.5 58.5 + - + +
21J HIS* 3.2 28.5 + - - +
28J ASP* 3.7 23.4 + - - +
31J LEU* 4.4 9.1 - - - +
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 4.1 15.0 + - - +
14C SER* 4.7 0.7 + - - -
16C TRP* 2.9 26.0 + - - -
56C GLN 3.0 10.6 + - - -
57C TRP 3.5 8.1 - - - +
59C ARG* 1.3 101.9 + - - +
61C VAL* 1.3 56.8 + - - +
63C ARG* 3.0 12.4 + - - +
64C GLU* 2.8 34.3 + - - +
20J VAL* 4.1 13.3 - - + +
21J HIS* 3.2 21.4 + - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.6 22.4 - - - +
607A PGV 3.8 25.7 + - - +
57C TRP* 3.1 25.1 + - + +
58C TRP* 3.1 18.0 + - + +
60C ASP* 1.3 76.8 - - - +
62C ILE* 1.3 53.4 + - - +
64C GLU* 3.6 6.9 + - - +
65C SER* 2.6 33.1 + - - -
71C HIS* 4.1 2.5 - - + -
307C PGV 3.4 43.7 - - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP 3.0 15.5 + - - +
59C ARG 2.9 7.5 + - - +
61C VAL* 1.3 75.8 - - - +
63C ARG* 1.3 58.9 + - - +
65C SER* 3.5 4.9 - - - -
66C THR* 2.9 36.5 + - - +
67C PHE* 3.6 4.5 + - + -
221C ARG* 3.5 39.9 - - + +
226C HIS* 3.8 28.0 - - + +
307C PGV 3.9 15.5 - - + -
309C CDL 3.9 44.0 - - + +
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 2.9 36.0 + - - +
60C ASP* 3.0 17.7 + - - +
62C ILE* 1.3 76.1 - - - +
64C GLU* 1.3 57.4 + - - +
67C PHE* 3.1 17.3 + - + +
68C GLN* 2.9 30.7 + - - +
309C CDL 3.1 44.0 + - - +
12J PHE* 3.4 29.3 - - + -
20J VAL* 2.7 45.1 + - + -
21J HIS 3.8 0.2 - - - -
24J GLY* 3.8 8.3 - - - +
28J ASP* 2.7 42.4 + - - -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 2.8 38.2 + - - -
607A PGV 2.8 23.5 + - - +
9C HIS* 3.4 24.6 + - + +
11C VAL* 3.5 9.0 - - - +
12C ASN 5.0 0.9 + - - -
60C ASP 2.8 20.4 + - - +
61C VAL* 3.7 6.9 - - - +
63C ARG* 1.3 73.1 - - - +
65C SER* 1.3 58.5 + - - +
68C GLN* 3.4 23.3 - - - +
69C GLY 3.5 2.3 + - - -
70C HIS* 3.0 32.6 + - + +
71C HIS* 4.7 0.7 - - - -
20J VAL* 3.7 18.3 - - + +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL 2.6 22.6 + - - -
62C ILE* 3.2 5.2 + - - -
63C ARG 3.2 0.4 - - - -
64C GLU* 1.3 78.1 - - - +
66C THR* 1.3 68.8 + - - +
67C PHE 3.3 0.7 - - - -
69C GLY* 3.2 21.8 + - - +
70C HIS 4.5 1.1 - - - +
71C HIS* 3.4 36.0 + - - +
307C PGV 3.3 36.5 + - - -
14F THR* 4.9 0.3 - - - +
17F GLU* 4.8 2.8 - - - +
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 2.9 13.0 + - - +
65C SER* 1.3 76.6 + - - +
67C PHE* 1.3 79.5 + - + +
221C ARG* 2.9 22.0 + - - -
226C HIS* 3.8 26.9 - - + +
307C PGV 2.7 30.8 + - - +
12F GLN* 4.6 2.6 - - - +
14F THR* 4.1 1.7 - - - +
5J VAL* 4.2 10.1 - - + -
9J GLN* 3.2 24.1 + - - +
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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