Contacts of the helix formed by residues 28 - 61 (chain C) in PDB entry 5FN2
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 ASP 28 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR 5.1 1.2 - - - +
25C VAL 2.8 11.9 + - - +
27C GLY* 1.3 70.2 + - - +
29C PRO* 1.3 72.5 - - + +
30C LEU* 3.2 3.1 - - + +
31C ARG* 3.0 67.0 + - + +
32C VAL* 3.3 5.4 + - - +
111C PRO 5.6 0.7 - - - +
112C ILE* 5.4 5.5 - - + +
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Residues in contact with PRO 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 3.8 11.7 - - + -
80B LYS* 3.8 31.0 - - + +
83B ILE* 3.5 42.1 - - + +
27C GLY 2.9 10.0 - - - +
28C ASP* 1.3 80.4 - - + +
30C LEU* 1.3 62.8 + - + +
32C VAL* 3.2 4.7 + - + +
33C ILE* 2.9 36.0 + - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 3.8 21.7 - - + +
28C ASP* 3.2 2.2 - - + -
29C PRO* 1.3 84.3 - - + +
31C ARG* 1.3 55.7 + - + +
33C ILE* 3.2 13.0 + - + +
34C ILE* 2.9 47.7 + - + +
101C LEU* 5.1 21.3 - - + -
111C PRO* 4.3 14.1 - - + -
112C ILE* 3.6 43.5 - - + -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ASN* 5.7 1.8 + - - -
24C THR* 2.6 46.3 + - - +
25C VAL* 3.4 13.7 - - + +
28C ASP* 3.0 47.6 + - + +
30C LEU* 1.3 75.2 - - - +
32C VAL* 1.3 58.7 - - - +
34C ILE* 3.2 9.8 + - + +
35C LEU* 2.9 26.9 + - - +
112C ILE* 4.9 13.8 - - + +
116C GLN* 3.4 34.5 + - + +
120C VAL* 3.4 30.9 - - + +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.2 28.9 - - + -
86B PHE* 5.5 5.2 - - + -
21C PHE* 4.2 22.7 - - + -
25C VAL* 3.3 27.3 - - + +
26C ALA 4.4 6.1 - - - +
28C ASP 3.8 8.3 - - - +
29C PRO* 3.2 10.0 + - + +
31C ARG* 1.3 80.2 - - - +
33C ILE* 1.3 59.5 + - + +
35C LEU* 3.2 8.0 + - + +
36C VAL* 2.9 38.2 + - + +
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 3.7 28.0 - - + +
82B VAL* 3.9 23.6 - - + -
83B ILE* 4.9 2.5 - - + +
86B PHE* 4.1 21.3 - - + -
419B CYS* 5.0 21.5 - - + -
423B LEU* 6.3 4.7 - - + -
29C PRO* 2.9 22.2 + - + +
30C LEU* 3.2 14.6 + - + +
32C VAL* 1.3 76.3 - - + +
34C ILE* 1.3 59.4 + - + +
36C VAL* 3.2 10.1 + - + +
37C ALA* 2.9 29.7 + - + +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 2.9 40.8 + - + +
31C ARG* 3.5 11.2 - - + +
33C ILE* 1.3 78.7 - - + +
35C LEU* 1.3 55.9 + - - +
37C ALA* 3.2 4.3 + - - -
38C GLY* 2.9 15.2 + - - -
90C TYR* 2.2 47.1 + - + +
94C LEU* 4.1 16.4 - - + -
112C ILE* 5.4 1.8 - - + -
117C MET* 3.9 39.9 - - + +
120C VAL* 3.2 19.5 - - + -
121C SER* 4.5 0.6 - - - +
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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
----------------------------------------------------------
21C PHE* 3.9 31.6 - - + -
25C VAL* 5.0 4.3 - - + -
31C ARG 2.9 12.0 + - - +
32C VAL* 3.4 12.8 - - + +
34C ILE* 1.3 76.7 - - - +
36C VAL* 1.3 65.8 + - + +
38C GLY 3.2 0.3 + - - -
39C ALA* 2.9 18.3 + - + +
120C VAL* 3.7 14.8 - - + +
123C LEU* 3.8 20.6 - - + -
124C SER* 2.8 57.6 - - - +
127C ILE* 5.0 13.2 - - + -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.6 15.0 - - + -
412B VAL* 4.5 3.7 - - + +
415B LEU* 3.9 37.7 - - + -
416B ILE* 3.2 28.3 - - + +
419B CYS* 5.6 2.2 - - + -
32C VAL* 2.9 26.9 + - + +
33C ILE* 3.4 12.6 - - + +
35C LEU* 1.3 85.4 - - + +
37C ALA* 1.3 56.5 + - - +
39C ALA* 3.2 9.8 + - - +
40C PHE 2.9 24.6 + - - -
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 3.9 12.3 - - + -
33C ILE* 2.9 14.8 + - + +
34C ILE* 3.4 10.3 - - - +
36C VAL* 1.3 77.2 - - - +
38C GLY* 1.3 58.1 + - - +
40C PHE* 3.2 4.1 + - + +
41C PHE* 2.9 39.2 + - + -
90C TYR* 3.4 18.4 - - + +
94C LEU* 6.0 0.2 - - + -
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE 2.9 11.4 + - - -
35C LEU 3.2 0.6 + - - -
37C ALA* 1.3 75.7 - - - +
39C ALA* 1.3 58.1 + - - +
41C PHE 3.2 1.6 + - - -
42C TRP* 2.9 13.5 + - - +
90C TYR* 3.3 21.5 - - - -
121C SER* 4.9 0.4 - - - -
124C SER* 3.0 17.0 - - - -
125C PHE* 2.7 32.7 - - - -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B VAL* 4.4 10.1 - - + -
35C LEU* 2.9 10.8 + - + +
36C VAL* 3.2 12.8 + - - +
38C GLY* 1.3 76.7 - - - +
40C PHE* 1.3 57.3 + - - +
42C TRP* 3.2 4.3 + - - +
43C LEU* 2.9 34.9 + - - +
124C SER* 2.8 13.7 + - - +
127C ILE* 5.8 2.7 - - + -
128C ILE* 3.8 31.4 - - + +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B VAL* 4.0 12.7 - - + +
413B ALA* 5.4 2.0 - - - -
416B ILE* 3.3 49.8 - - + -
441B PHE* 4.3 17.5 - + - -
445B PHE* 3.4 27.1 - + - -
36C VAL 2.9 4.9 + - - -
37C ALA* 3.3 7.4 - - + +
39C ALA* 1.3 76.7 - - - +
41C PHE* 1.3 84.0 + + - +
43C LEU* 3.2 4.9 + - - +
44C VAL* 2.9 56.0 + - + +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA* 2.9 25.8 + - + +
38C GLY 3.2 10.1 + - - +
40C PHE* 1.3 98.4 - + - +
42C TRP* 1.3 57.2 + - - +
44C VAL* 3.2 6.7 + - - +
45C SER* 2.9 25.1 + - - -
86C PHE* 3.2 45.4 - + + -
89C ALA* 4.2 9.0 - - + -
90C TYR* 3.6 41.3 - + + -
93C LEU* 3.8 26.7 - - + -
125C PHE* 3.9 11.7 - - + -
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Residues in contact with TRP 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B MET* 4.9 0.2 - - + -
467B ILE* 4.3 11.9 - - + -
38C GLY 2.9 7.6 + - - +
39C ALA 3.2 7.6 + - - +
41C PHE* 1.3 76.1 - - - +
43C LEU* 1.3 85.5 + - + +
45C SER* 2.5 24.0 + - - -
46C LEU* 2.9 45.9 + - + -
83C GLN* 2.8 36.3 + - + -
125C PHE* 3.4 39.9 - + + -
128C ILE* 3.3 31.4 - - + -
129C SER* 3.3 29.6 - - - -
132C PHE* 3.6 38.6 - + + -
171C HIS* 4.7 0.2 - + - -
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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
----------------------------------------------------------
409B ALA* 4.3 16.6 - - + +
412B VAL* 3.1 46.4 - - + -
413B ALA 5.1 0.2 - - - +
445B PHE* 3.7 20.0 - - + -
453B VAL* 5.2 1.6 - - - +
39C ALA 2.9 15.4 + - - +
40C PHE* 3.3 8.3 - - - +
42C TRP* 1.3 91.8 - - + +
44C VAL* 1.3 58.3 + - - +
46C LEU* 3.2 5.6 + - + +
47C LEU* 2.9 28.8 + - - +
128C ILE* 3.9 7.4 - - + -
132C PHE* 3.4 35.9 - - + -
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE* 3.7 10.8 - - + -
40C PHE* 2.9 63.4 + - + +
41C PHE* 3.2 8.0 + - - +
43C LEU* 1.3 74.4 - - - +
45C SER* 1.3 58.8 + - - +
47C LEU* 3.2 11.4 + - + +
48C LEU* 2.9 36.7 + - + +
86C PHE* 3.5 23.1 - - + -
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE 2.9 12.9 + - - -
42C TRP* 2.5 21.7 + - - -
44C VAL* 1.3 77.2 - - - +
46C LEU* 1.3 61.6 + - - +
48C LEU* 3.2 4.8 + - - +
49C ALA* 2.9 29.7 + - - +
79C SER 5.7 0.4 - - - -
82C LEU* 3.9 6.9 - - - +
83C GLN* 3.3 33.4 - - - +
86C PHE* 3.7 34.7 - - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B VAL* 3.7 22.9 - - + -
456B PHE* 3.9 18.4 - - + -
457B MET* 3.6 20.4 - - - -
467B ILE* 3.5 26.5 - - + -
42C TRP* 2.9 48.1 + - + +
43C LEU* 3.4 10.3 - - + +
45C SER* 1.3 84.3 + - - +
47C LEU* 1.3 51.6 + - - +
49C ALA* 3.2 6.7 + - + +
50C SER* 2.6 38.2 + - - -
79C SER* 4.8 1.8 - - - -
83C GLN* 5.8 1.1 - - - +
132C PHE* 3.9 5.4 - - + -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B VAL* 6.2 4.3 - - + -
445B PHE* 5.4 10.5 - - + -
448B ALA* 3.6 31.4 - - + -
449B THR* 5.7 0.4 - - - +
452B LEU* 4.5 2.5 - - + -
453B VAL* 3.8 17.0 - - + +
43C LEU 2.9 12.9 + - - +
44C VAL* 3.3 15.0 - - + +
46C LEU* 1.3 75.7 - - - +
48C LEU* 1.3 78.5 - - + +
50C SER* 2.6 27.9 + - - +
51C VAL* 2.9 33.6 + - + +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 2.9 22.7 + - + +
45C SER 3.2 6.0 + - - +
47C LEU* 1.3 89.8 - - + +
49C ALA* 1.3 59.2 + - - +
51C VAL* 3.2 7.9 + - + +
52C VAL* 2.9 33.8 + - + +
82C LEU* 3.7 15.9 - - + -
86C PHE* 3.6 34.3 - - + -
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B PHE* 5.6 2.7 - - + -
45C SER 2.9 13.2 + - - +
46C LEU* 3.4 9.9 - - + +
48C LEU* 1.3 76.4 - - - +
50C SER* 1.3 58.5 + - - +
52C VAL* 3.2 9.2 + - - +
53C TRP* 2.9 29.4 + - - +
75C GLY* 4.6 4.9 - - - +
78C VAL* 4.5 4.5 - - + +
79C SER* 3.5 41.5 - - - +
82C LEU* 3.6 10.7 - - + +
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Residues in contact with SER 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 3.1 38.5 - - - +
453B VAL* 3.3 16.8 + - - -
456B PHE* 4.8 12.6 - - - -
46C LEU* 2.6 20.2 + - - +
47C LEU* 2.6 22.9 + - - -
49C ALA* 1.3 73.5 - - - +
51C VAL* 1.3 58.7 + - - +
53C TRP* 3.2 9.5 + - - +
54C PHE* 2.9 29.0 + - - +
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 4.0 21.1 - - + -
47C LEU* 2.9 40.9 + - + +
48C LEU* 3.3 11.4 - - + +
50C SER* 1.3 80.4 + - - +
52C VAL* 1.3 60.8 + - + +
54C PHE* 3.2 10.8 + - + +
55C ILE* 2.9 52.7 + - + +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 2.9 20.4 + - + +
49C ALA* 3.2 11.9 + - - +
51C VAL* 1.3 78.9 - - + +
53C TRP* 1.3 58.3 + - - +
55C ILE* 3.2 11.3 + - + +
56C LEU* 2.9 45.1 + - + +
74C PHE* 5.1 5.2 - - + -
75C GLY* 5.9 2.2 - - - -
78C VAL* 4.5 25.8 - - + -
82C LEU* 5.2 3.4 - - + -
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Residues in contact with TRP 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU 4.8 1.6 - - - -
455B PRO* 4.0 17.7 - - + -
456B PHE* 3.6 62.6 - + + -
459B GLN* 4.8 14.8 - - + -
49C ALA 2.9 13.2 + - - +
50C SER 3.2 9.8 + - - +
52C VAL* 1.3 77.2 - - - +
54C PHE* 1.3 77.4 + + + +
56C LEU* 3.2 9.5 + - + +
57C VAL* 2.9 56.7 + - + +
68C GLN* 4.8 5.5 + - + -
71C LEU* 4.0 21.1 - - + +
72C LEU* 3.5 35.6 - - + +
75C GLY* 4.4 9.6 - - - -
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B TYR* 4.3 15.7 - - + -
452B LEU* 4.1 28.0 - - + +
455B PRO* 5.6 2.2 - - + -
50C SER 2.9 13.2 + - - +
51C VAL* 3.2 15.0 - - + +
53C TRP* 1.3 91.3 - + + +
55C ILE* 1.3 67.8 + - + +
57C VAL* 3.2 4.6 + - + +
58C HIS* 2.9 76.7 + + + -
----------------------------------------------------------
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Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 2.9 40.7 + - + +
52C VAL* 3.2 11.4 + - + +
54C PHE* 1.3 84.6 - - + +
56C LEU* 1.3 63.8 + - + +
58C HIS* 3.2 4.7 + - - +
59C VAL* 2.9 44.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 2.9 29.6 + - + +
53C TRP* 3.4 13.0 - - + +
55C ILE* 1.3 85.3 - - + +
57C VAL* 1.3 62.1 + - - +
59C VAL* 3.6 3.6 + - + +
60C THR* 3.2 34.4 + - - +
71C LEU* 4.2 23.9 - - + +
74C PHE* 3.9 33.4 - - + -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 2.9 52.7 + - + +
54C PHE* 3.2 9.8 + - + +
56C LEU* 1.3 75.1 - - - +
58C HIS* 1.3 65.7 + - + +
61C ASP* 2.7 36.6 + - - -
62C ARG* 5.4 7.4 - - + +
68C GLN* 3.6 25.8 - - - +
71C LEU* 4.4 10.5 - - + -
----------------------------------------------------------
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Residues in contact with HIS 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 2.9 64.9 + + + +
55C ILE* 3.8 5.4 - - - +
57C VAL* 1.3 87.3 - - + +
59C VAL* 1.3 67.7 + - + +
60C THR 3.4 0.3 + - - -
61C ASP* 4.0 9.3 + - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 2.9 33.7 + - + +
56C LEU* 4.2 4.3 - - + +
58C HIS* 1.3 77.3 - - + +
60C THR* 1.3 65.1 + - - +
61C ASP* 5.1 0.5 - - - +
----------------------------------------------------------
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.2 21.9 + - - +
57C VAL 4.3 0.4 - - - -
59C VAL* 1.3 82.9 - - - +
61C ASP* 1.3 71.5 + - - +
63C SER* 5.1 1.6 + - - -
67C LEU* 3.9 30.5 - - + -
71C LEU* 4.5 11.0 - - + +
----------------------------------------------------------
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C VAL 2.7 24.0 + - - -
58C HIS* 4.0 7.2 + - - +
59C VAL 3.8 1.3 - - - +
60C THR* 1.3 86.7 - - - +
62C ARG* 1.3 74.5 + - - +
63C SER* 3.4 13.6 + - - +
67C LEU* 5.1 3.1 - - - +
68C GLN* 4.1 9.4 + - - -
71C LEU* 5.8 0.2 - - - +
----------------------------------------------------------
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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