Contacts of the helix formed by residues 43 - 74 (chain N) in PDB entry 6CP3
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 ILE 43 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N GLY* 5.6 0.2 - - - -
37N VAL* 4.5 9.9 - - + +
40N ASN* 3.3 36.8 - - - +
41N PRO 3.2 1.0 + - - -
42N SER* 1.3 79.6 - - - +
44N LYS* 1.3 61.8 + - - +
45N ASP 3.3 2.5 - - - -
46N THR* 2.9 34.1 + - + +
47N VAL* 3.0 41.6 + - + +
37O VAL* 3.5 24.0 - - + +
38O SER* 3.8 16.4 - - - -
41O PRO* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M THR* 3.4 39.9 + - - +
50M MET* 5.3 9.0 - - + -
37N VAL* 3.7 16.6 - - + -
41N PRO* 3.3 26.2 - - - +
42N SER* 3.7 0.8 - - - +
43N ILE* 1.3 78.8 - - - +
45N ASP* 1.3 57.8 + - - +
47N VAL* 3.8 9.4 - - + -
48N PHE* 2.9 40.6 + - + +
49N PRO* 3.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ILE 3.3 0.4 - - - -
44N LYS* 1.3 78.4 - - - +
46N THR* 1.3 62.4 + - - +
49N PRO* 3.6 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ILE* 2.9 22.0 + - + +
45N ASP* 1.3 83.4 + - - +
47N VAL* 1.3 68.2 + - + +
48N PHE 3.5 0.4 + - - -
49N PRO* 4.2 1.2 - - - +
50N MET* 3.6 22.3 + - + +
37O VAL* 3.9 21.3 - - + -
44O LYS* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N LEU* 3.8 24.2 - - + -
37N VAL* 5.6 1.8 - - + +
43N ILE* 3.0 46.7 + - + +
44N LYS* 3.8 8.7 - - + -
46N THR* 1.3 78.6 - - + +
48N PHE* 1.3 57.4 + - - +
49N PRO 3.6 0.2 - - - -
50N MET* 3.1 8.2 + - - +
51N ALA* 2.5 38.7 + - - +
34O ILE* 5.0 13.0 - - + +
37O VAL* 3.7 29.4 - - + -
38O SER* 4.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M MET* 4.2 26.5 - - + -
53M LEU* 4.9 20.0 - - + -
30N PHE* 5.7 3.8 - + - -
33N LEU* 4.1 23.1 - - + -
44N LYS* 2.9 27.4 + - + +
47N VAL* 1.3 77.6 - - + +
49N PRO* 1.3 67.8 - - + +
51N ALA* 3.4 5.9 + - + +
52N ILE* 3.0 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N LYS 3.8 1.6 - - - +
45N ASP* 3.6 24.9 - - - +
46N THR 4.2 0.9 - - - +
47N VAL 4.1 0.2 - - - -
48N PHE* 1.3 97.2 - - + +
50N MET* 1.3 56.4 + - - +
52N ILE* 3.4 11.5 - - + +
53N LEU* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N THR* 3.6 16.7 + - + +
47N VAL* 3.1 10.4 + - - +
49N PRO* 1.3 79.2 - - - +
51N ALA* 1.3 57.8 + - - +
53N LEU* 3.4 9.1 + - + +
54N GLY* 2.9 24.4 + - - -
30O PHE* 4.7 9.1 - - + -
33O LEU* 3.7 33.4 - - + -
34O ILE* 5.8 5.8 - - + -
37O VAL* 4.7 14.4 - - + -
44O LYS* 3.7 33.0 - - + +
48O PHE* 3.6 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 4.1 16.9 - - + +
30N PHE* 5.1 9.4 - - + -
33N LEU* 4.7 15.7 - - + -
47N VAL 2.5 21.7 + - - +
48N PHE* 3.4 8.3 + - + +
50N MET* 1.3 75.6 - - - +
52N ILE* 1.3 57.6 + - - +
54N GLY* 3.2 2.3 + - - -
55N PHE* 2.9 26.3 + - - +
30O PHE* 6.1 0.7 - - - -
34O ILE* 4.3 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M LEU* 5.6 5.8 - - + -
57M LEU* 5.2 11.2 - - + -
30N PHE* 5.2 6.5 - - + -
48N PHE* 3.0 40.6 + - + +
49N PRO* 3.4 12.8 - - + +
51N ALA* 1.3 73.0 - - - +
53N LEU* 1.3 62.8 + - - +
55N PHE* 3.4 18.8 + - + +
56N ALA* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N PRO 2.9 19.7 + - - +
50N MET* 3.4 9.4 - - - +
52N ILE* 1.3 77.8 - - - +
54N GLY* 1.3 57.2 + - - +
56N ALA* 3.1 9.2 + - + +
57N LEU* 3.0 56.3 + - + +
30O PHE* 4.6 5.6 - - + -
48O PHE* 5.3 9.6 - - + -
52O ILE* 4.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 5.3 5.4 - - - -
50N MET 2.9 15.5 + - - -
51N ALA* 3.2 3.8 + - - -
53N LEU* 1.3 71.8 - - - +
55N PHE* 1.3 58.6 + - - +
57N LEU* 3.7 11.8 - - - -
58N SER* 2.6 38.7 + - - -
30O PHE* 4.1 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M LEU* 3.5 44.9 - - + -
61M THR* 5.6 0.2 - - + -
26N ILE* 3.6 44.2 - - + +
29N VAL* 5.0 4.5 - - + +
30N PHE* 3.8 22.4 - + + -
51N ALA 2.9 13.3 + - - +
52N ILE* 3.5 20.2 - - + +
54N GLY* 1.3 76.4 - - - +
56N ALA* 1.3 62.4 + - + +
58N SER* 3.9 3.6 - - - -
59N GLU* 2.8 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N ILE 3.0 17.1 + - - +
53N LEU* 3.1 11.0 + - + +
55N PHE* 1.3 85.1 - - + +
57N LEU* 1.3 57.7 + - + +
59N GLU* 3.2 5.5 + - - +
60N ALA* 3.0 27.5 + - - +
63N LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N LEU* 3.0 46.0 + - + +
54N GLY* 3.7 8.1 - - - -
56N ALA* 1.3 75.7 - - + +
58N SER* 1.3 58.3 + - - +
60N ALA* 4.3 14.0 - - + +
61N THR* 4.9 3.8 - - - +
26O ILE* 4.3 2.6 - - - +
30O PHE* 3.6 31.0 - - + -
52O ILE* 5.0 8.1 - - + -
55O PHE* 3.5 42.9 - - + -
59O GLU* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N ALA* 4.9 4.0 - - - +
26N ILE* 4.2 15.7 - - - -
29N VAL* 5.4 0.6 - - - +
54N GLY 2.6 22.4 + - - -
55N PHE 3.9 2.7 - - - -
57N LEU* 1.3 77.5 - - - +
59N GLU* 1.3 58.1 + - - +
60N ALA 3.2 1.8 - - - -
61N THR* 2.8 28.9 + - - -
62N GLY 4.2 0.3 + - - -
23O GLY* 4.8 7.3 - - - +
26O ILE* 4.1 14.8 - - - +
27O ALA* 3.9 29.0 + - - -
30O PHE* 4.4 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M THR* 3.3 24.9 - - - +
64M PHE* 5.0 4.7 - - - -
19N LEU* 6.1 1.0 - - - +
22N ALA* 4.9 6.1 - - - +
26N ILE* 3.3 31.5 - - + +
55N PHE* 2.8 36.6 + - + +
56N ALA* 3.7 4.9 - - - +
58N SER* 1.3 73.4 - - - +
60N ALA* 1.3 59.6 + - - +
61N THR 3.2 0.9 - - - -
62N GLY* 3.2 9.1 + - - +
63N LEU* 2.9 53.2 + - + +
66N LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N ALA 3.0 14.1 + - - +
57N LEU* 4.3 13.9 - - + +
58N SER 3.2 0.4 - - - -
59N GLU* 1.3 76.9 - - - +
61N THR* 1.3 58.1 + - + +
63N LEU* 3.7 11.0 - - - +
64N PHE* 2.9 50.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N ALA* 4.3 3.5 - - - +
57N LEU 4.9 3.6 - - - +
58N SER 2.8 22.7 + - - +
60N ALA* 1.3 78.0 - - + +
62N GLY* 1.3 57.5 + - - +
64N PHE* 3.3 12.6 + - + +
65N CYS* 2.9 26.5 + - - +
19O LEU* 3.8 27.1 - - + +
22O ALA* 5.8 2.0 - - + -
23O GLY* 4.0 17.7 - - - +
26O ILE* 4.5 16.4 - - + -
59O GLU* 4.3 19.7 - - + +
62O GLY 6.6 0.2 - - - -
63O LEU* 5.9 3.6 - - + -
66O LEU* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N GLY 4.9 2.5 - - - -
19N LEU* 4.7 20.2 - - - +
22N ALA* 4.9 6.2 - - - +
58N SER 4.2 0.8 + - - -
59N GLU* 3.2 15.1 + - - +
61N THR* 1.3 80.2 + - - +
63N LEU* 1.3 61.1 + - - +
65N CYS* 3.2 9.2 + - - +
66N LEU* 3.0 32.9 + - - +
19O LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M PHE* 4.4 15.9 - - + -
59N GLU* 2.9 43.1 + - + +
60N ALA* 3.7 10.1 - - - +
62N GLY* 1.3 75.2 - - - +
64N PHE* 1.3 66.9 + - + +
66N LEU* 3.4 19.9 + - + +
67N MET* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N ALA* 2.9 35.3 + - + +
61N THR* 3.5 10.8 - - + +
63N LEU* 1.3 77.7 - - + +
65N CYS* 1.3 57.6 + - - +
67N MET* 3.3 24.4 - - + +
68N VAL* 3.0 35.6 + - - +
19O LEU* 5.6 0.7 - - + -
63O LEU* 4.6 23.1 - - + -
66O LEU* 4.4 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N SER 3.7 9.8 - - - +
16N THR 4.3 3.6 - - - -
18N GLY* 3.6 33.2 - - - -
19N LEU* 4.1 1.8 - - - -
61N THR 2.9 14.7 + - - +
62N GLY* 3.4 12.8 - - - +
63N LEU 3.2 0.4 - - - -
64N PHE* 1.3 76.6 - - - +
66N LEU* 1.3 61.1 + - - +
68N VAL* 3.2 9.5 + - - +
69N SER* 2.9 22.7 + - - -
16O THR* 3.7 23.1 - - - -
19O LEU* 4.2 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M PHE* 3.8 37.2 - - + -
67M MET* 4.7 6.1 - - + -
68M VAL* 4.3 19.7 - - + -
16N THR 5.6 1.6 - - - +
19N LEU* 4.7 17.7 - - + -
59N GLU* 5.9 0.4 - - - +
62N GLY 3.0 28.8 + - - +
63N LEU* 3.7 31.4 - - + +
65N CYS* 1.3 75.2 - - + +
67N MET* 1.3 61.1 + - - +
69N SER* 3.3 11.3 - - - -
70N PHE* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N LEU 3.0 17.6 + - - +
64N PHE* 3.3 42.4 - - + +
66N LEU* 1.3 77.1 - - - +
68N VAL* 1.3 73.0 + - + +
70N PHE* 3.3 6.1 + - - +
71N LEU* 3.0 44.8 + - + +
66O LEU* 5.0 3.1 - - + -
70O PHE* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N SER* 5.1 4.5 - - - -
64N PHE 3.0 19.5 + - - +
65N CYS* 3.4 10.8 - - - +
67N MET* 1.3 90.3 - - + +
69N SER* 1.3 57.8 + - - +
71N LEU* 3.3 18.5 + - + +
72N LEU* 2.9 34.3 + - + +
12O ALA* 5.2 2.5 - - + +
16O THR* 4.8 15.9 - - + +
66O LEU* 5.1 12.1 - - + -
69O SER* 4.1 20.6 - - - +
70O PHE* 4.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M VAL* 4.5 16.4 - - - +
12N ALA* 3.5 22.5 + - - +
15N SER* 3.9 24.5 - - - -
16N THR* 4.1 8.0 + - - +
65N CYS 2.9 13.6 + - - -
66N LEU* 3.3 17.5 - - - -
67N MET 3.2 0.2 - - - -
68N VAL* 1.3 77.4 - - - +
70N PHE* 1.3 56.5 + - - +
72N LEU 3.6 0.3 + - - -
73N LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M LEU* 5.1 8.1 - - + -
66N LEU 3.0 14.7 + - - +
67N MET* 4.0 7.0 - - - +
68N VAL 3.3 0.4 - - - -
69N SER* 1.3 77.0 - - - +
71N LEU* 1.3 64.2 + - - +
73N LEU* 3.0 25.9 + - + +
74N PHE* 2.8 50.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N LYS* 4.7 1.9 + - - -
67N MET* 3.0 40.4 + - + +
68N VAL* 3.5 26.7 - - + +
70N PHE* 1.3 81.2 - - + +
72N LEU* 1.3 61.6 + - + +
74N PHE 3.1 24.4 - - - +
70O PHE* 5.2 9.6 - - + -
73O LEU* 3.7 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N LYS* 3.1 40.8 - - + +
11N GLY* 3.4 28.3 - - - +
12N ALA* 4.1 9.0 - - + +
15N SER* 3.9 5.6 - - - +
68N VAL* 2.9 20.0 + - + +
69N SER 4.1 3.4 - - - +
71N LEU* 1.3 78.3 - - + +
73N LEU* 1.3 63.1 + - - +
74N PHE 3.2 0.9 - - - -
9O TYR* 3.6 44.6 - - + +
12O ALA* 4.1 6.3 - - + +
13O GLY* 3.8 11.9 - - - +
73O LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LYS* 6.3 1.1 - - - -
68M VAL* 5.4 6.3 - - + -
71M LEU* 3.7 36.3 - - + +
72M LEU* 3.7 25.4 - - + -
75M GLY 6.0 4.0 - - - -
8N LYS* 4.5 2.4 - - - -
9N TYR* 3.2 48.9 + - + -
12N ALA* 3.8 13.2 - - + +
69N SER* 2.9 20.0 + - - +
70N PHE* 3.0 26.2 + - + +
72N LEU* 1.3 78.8 - - - +
74N PHE* 1.3 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N LYS* 2.8 30.0 + - - +
9N TYR* 5.9 2.5 - - - -
70N PHE* 2.8 35.0 + + + +
71N LEU* 3.1 19.7 - - - +
72N LEU 3.2 0.2 - - - -
73N LEU* 1.3 83.0 - - + +
----------------------------------------------------------
Back to top of page
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