Contacts of the helix formed by residues 43 - 72 (chain F) in PDB entry 4E45
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 43 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLN 4.2 0.4 + - - -
42F PHE* 1.3 76.0 - - - +
44F LYS* 1.3 65.4 + - - +
45F GLN* 3.4 13.8 + - - +
46F THR* 2.9 37.6 + - - -
47F ILE* 3.2 12.5 + - - +
64G ARG* 3.6 27.5 - - - +
65G VAL 2.9 11.8 + - - -
66G ASP* 3.5 24.9 + - - -
67G VAL 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 5.3 1.7 + - - -
42F PHE 5.0 3.2 + - - +
43F SER* 1.3 72.9 - - - +
45F GLN* 1.3 65.2 + - - +
47F ILE* 3.4 24.6 + - + +
48F ALA* 3.0 26.0 + - - +
64G ARG* 5.2 0.6 - - - +
775J CYS* 4.0 20.3 - - + +
778J GLU* 3.7 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F SER* 3.1 15.4 + - - +
44F LYS* 1.3 82.0 + - - +
46F THR* 1.3 59.2 + - - +
48F ALA* 3.4 6.5 + - - -
49F ALA* 2.9 29.5 + - - +
64G ARG* 4.8 3.8 + - - -
66G ASP* 5.3 0.7 - - - +
67G VAL* 3.5 20.0 - - + -
768J MET* 3.4 32.7 - - + +
771J GLU* 3.1 44.6 + - - +
773J GLY 4.5 7.5 + - - -
775J CYS* 4.0 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.8 16.2 - - + -
43F SER* 2.9 24.3 + - - -
45F GLN* 1.3 74.2 - - - +
47F ILE* 1.3 60.7 + - - +
49F ALA* 3.2 3.9 + - - +
50F ILE* 2.9 42.2 + - + +
65G VAL* 3.0 35.9 + - + -
66G ASP 3.2 16.1 - - - -
67G VAL* 3.3 5.8 + - - -
70G LEU* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 4.2 16.2 - - + +
27F VAL* 3.9 6.4 - - + +
28F GLY* 4.0 30.1 - - - +
31F CYS* 4.2 18.4 - - + -
32F GLU 6.0 0.2 - - - +
42F PHE* 3.8 27.4 - - + +
43F SER 3.2 14.1 + - - +
44F LYS* 3.6 27.8 - - + +
46F THR* 1.3 77.9 - - - +
48F ALA* 1.3 57.6 + - - +
50F ILE* 3.3 8.3 + - - +
51F SER* 2.8 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 4.1 7.8 - - - +
44F LYS 3.0 14.6 + - - +
45F GLN 3.5 7.9 - - - +
46F THR 3.3 0.2 - - - -
47F ILE* 1.3 76.7 - - - +
49F ALA* 1.3 56.8 - - - +
51F SER* 3.2 3.6 + - - -
52F GLU* 3.0 23.6 + - - +
764J MET* 3.6 13.3 - - + +
768J MET* 4.1 1.8 - - - -
775J CYS* 3.9 9.9 - - - -
777J TYR* 3.6 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLN 2.9 17.5 + - - +
46F THR* 3.6 2.9 - - - +
48F ALA* 1.3 72.5 - - - +
50F ILE* 1.3 60.2 + - - +
52F GLU 3.4 0.3 + - - -
53F LEU* 2.9 29.6 + - - +
67G VAL* 4.7 2.7 - - + -
70G LEU* 3.4 24.5 - - + -
761J LEU* 3.6 7.2 - - + +
764J MET* 3.9 12.5 - - - +
765J ILE* 4.1 16.8 - - + -
768J MET* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F VAL* 3.6 18.8 - - + -
31F CYS* 4.1 17.9 - - - -
42F PHE* 4.7 2.0 - - + -
46F THR* 2.9 37.3 + - + +
47F ILE 3.8 3.6 - - - +
49F ALA* 1.3 74.8 - - - +
51F SER* 1.3 57.7 + - - +
53F LEU* 3.3 8.7 + - + +
54F THR* 2.9 37.8 + - - +
46G VAL* 4.1 16.6 - - + -
49G ALA* 4.2 16.6 - - + -
50G ALA* 4.2 20.2 - - - +
70G LEU* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LYS 5.2 0.4 - - - -
23F VAL* 3.7 4.7 - - - +
24F HIS* 3.3 41.6 - - - -
27F VAL* 3.4 24.5 - - - +
47F ILE 2.8 15.7 + - - -
48F ALA 3.5 7.2 - - - -
50F ILE* 1.3 74.1 - - - +
52F GLU* 1.3 61.8 + - - +
54F THR* 3.1 3.8 + - - -
55F PHE* 2.9 27.4 + - - +
777J TYR* 4.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LYS* 2.9 32.7 + - - +
48F ALA 3.0 11.0 + - - +
51F SER* 1.3 74.3 - - - +
53F LEU* 1.3 57.2 - - - +
55F PHE* 3.4 6.4 + - - +
56F ARG* 2.8 70.4 + - - +
761J LEU* 3.8 8.1 - - + -
764J MET* 3.6 30.7 - - + -
777J TYR* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ALA 2.9 18.6 + - - +
50F ILE* 3.3 12.3 - - + +
52F GLU* 1.3 77.9 - - - +
54F THR* 1.3 52.0 + - - +
56F ARG* 3.3 6.0 + - + +
57F GLN* 2.8 36.2 + - - +
45G PHE* 3.7 17.9 - - + -
49G ALA* 4.3 9.9 - - + -
74G LEU* 4.1 15.9 - - + -
77G LEU* 3.7 28.7 - - + -
78G LEU* 3.8 33.2 - - + +
761J LEU* 3.4 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.9 17.7 - - + -
27F VAL* 4.2 1.2 - - - +
50F ILE* 2.9 19.4 + - - +
51F SER 3.1 4.2 + - - -
53F LEU* 1.3 72.5 - - - +
55F PHE* 1.3 68.3 + - - +
57F GLN* 3.2 2.3 + - - +
58F CYS* 3.0 29.1 + - - -
10G PHE* 4.1 7.6 - - + -
42G LEU* 3.9 22.8 - - + +
45G PHE* 3.8 17.1 - - + -
46G VAL* 3.4 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLN* 4.1 16.6 - - + -
19F LEU* 4.1 11.7 - - + -
20F LYS* 3.8 53.2 - - + -
23F VAL* 4.1 11.0 - - + +
51F SER 2.9 13.2 + - - +
52F GLU* 3.6 11.9 - - - +
54F THR* 1.3 78.0 - - - +
56F ARG* 1.3 72.4 + - + +
58F CYS* 3.3 18.9 + - - +
59F GLU 3.6 2.8 + - - -
18G LEU* 3.6 29.8 - - + -
21G LEU* 4.1 20.0 - - + -
22G HIS* 4.6 14.0 - + - -
777J TYR* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU* 2.8 55.4 + - - +
53F LEU* 3.8 5.6 - - + +
55F PHE* 1.3 84.7 - - + +
57F GLN* 1.3 60.7 + - - +
59F GLU* 3.0 23.1 + - - +
60F ASN* 3.5 10.6 + - - +
756J ARG 4.4 1.4 + - - -
757J HIS* 3.4 72.2 + - + +
760J GLY* 4.0 24.4 + - - -
761J LEU* 4.5 7.6 - - - +
764J MET* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LEU 2.8 21.4 + - - +
54F THR 3.2 4.5 + - - +
56F ARG* 1.3 72.3 - - - +
58F CYS* 1.3 65.3 + - - +
60F ASN* 3.0 26.5 + - - +
61F PHE* 2.8 62.4 + - + -
42G LEU* 5.8 0.2 - - + -
45G PHE* 3.7 28.9 - - + -
78G LEU* 3.6 19.3 - - + +
81G PHE* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 5.7 0.4 - - - -
54F THR* 3.0 22.8 + - - -
55F PHE* 3.4 11.9 - - - +
57F GLN* 1.3 76.1 - - - +
59F GLU* 1.3 58.2 + - - +
61F PHE* 3.7 7.8 - - - +
62F ALA* 2.9 30.3 + - - +
18G LEU* 4.1 36.8 - - + -
19G LEU* 3.9 7.8 - - + +
22G HIS* 4.2 5.8 + - - +
42G LEU* 3.8 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F PHE 3.6 2.2 + - - +
56F ARG* 3.0 13.7 + - - +
58F CYS* 1.3 79.9 - - - +
60F ASN* 1.3 63.0 + - - +
62F ALA* 3.4 0.9 + - - +
63F LYS* 3.1 53.5 + - + +
22G HIS* 3.4 43.0 + - + +
753J ASP* 4.9 6.8 - - + +
757J HIS* 2.9 31.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ARG 3.5 8.3 + - - -
57F GLN* 3.0 34.1 + - - +
59F GLU* 1.3 74.3 - - - +
61F PHE* 1.3 66.3 + - + +
62F ALA 3.3 0.3 + - - -
63F LYS* 3.4 3.8 + - - +
64F ASP* 3.1 31.3 + - - +
78G LEU* 4.8 4.6 - - - +
81G PHE 5.7 1.1 - - - +
88H ARG* 6.4 0.2 - - - +
753J ASP* 4.5 4.3 - - - +
754J ARG* 3.6 37.7 + - - +
757J HIS* 3.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F GLN* 2.8 56.9 + - + +
58F CYS* 3.7 6.7 - - - +
60F ASN* 1.3 74.1 - - - +
62F ALA* 1.3 53.7 + - - +
64F ASP* 3.2 2.6 + - - +
65F LEU* 2.8 40.9 + - - +
85F LEU* 3.8 28.0 - - + +
19G LEU* 4.5 1.1 - - + -
38G MET* 3.7 31.4 - - + -
41G LEU* 4.1 21.3 - - + -
42G LEU* 3.9 24.0 - - + -
45G PHE* 4.5 7.0 - + + -
81G PHE* 4.1 29.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F CYS 2.9 18.0 + - - +
59F GLU 3.6 4.5 - - - +
60F ASN 3.2 0.2 - - - -
61F PHE* 1.3 76.9 - - - +
63F LYS* 1.3 61.2 + - - +
65F LEU* 3.4 1.9 + - - -
66F GLU* 3.2 18.0 + - - +
19G LEU* 3.7 40.2 - - + +
22G HIS* 3.8 13.2 - - + -
23G PHE* 3.2 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLU* 3.1 45.5 + - + +
60F ASN* 4.1 3.8 - - - +
62F ALA* 1.3 73.2 - - - +
64F ASP* 1.3 66.4 + - - +
66F GLU* 3.7 11.0 + - - +
67F MET* 3.2 31.3 + - - +
22G HIS* 3.8 26.7 - - - +
24G LYS* 5.6 6.3 - - + +
753J ASP* 3.9 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ASN* 3.1 20.8 + - - +
63F LYS* 1.3 77.8 - - - +
65F LEU* 1.3 56.7 + - - +
67F MET* 3.0 5.9 + - - +
68F PHE* 2.8 47.0 + - + -
85F LEU* 3.7 24.1 - - + +
87F ARG* 5.2 1.6 + - - -
81G PHE 5.7 1.0 - - - +
87H ARG* 2.9 43.6 + - - +
88H ARG* 3.8 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F PHE 2.8 22.2 + - - +
62F ALA* 3.7 3.8 - - - +
64F ASP* 1.3 75.8 - - - +
66F GLU* 1.3 56.6 - - - +
68F PHE* 3.4 5.2 + - - +
69F ALA* 3.0 28.9 + - - +
77F ILE* 3.7 28.3 - - + +
81F ASP* 3.6 35.1 - - + +
82F VAL* 3.6 10.5 - - + +
85F LEU* 3.6 22.0 - - + -
19G LEU* 4.2 18.8 - - + -
30G VAL* 6.0 0.7 - - + -
38G MET* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ALA 3.2 14.4 + - - +
63F LYS* 3.9 10.0 - - - +
65F LEU* 1.3 75.5 - - - +
67F MET* 1.3 63.1 + - + +
69F ALA* 3.4 2.9 + - - +
70F ARG* 3.0 27.5 + - + +
74F ARG 5.1 0.2 - - - +
77F ILE* 3.9 9.6 - - - +
23G PHE* 3.4 16.6 - - + +
24G LYS* 2.9 28.7 + - - +
25G ASP* 3.1 21.9 + - + +
28G THR* 2.5 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LYS* 3.2 19.4 + - - +
64F ASP* 3.0 6.5 + - - +
66F GLU* 1.3 79.8 - - + +
68F PHE* 1.3 60.8 + - + +
70F ARG* 3.3 6.8 + - - +
71F HIS* 2.9 29.5 + - - +
84H LEU* 4.2 16.5 - - + +
87H ARG* 3.9 43.7 - - + +
93H LEU* 5.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ASP* 2.8 30.9 + - + +
65F LEU* 3.8 5.2 - - - +
67F MET* 1.3 75.4 - - - +
69F ALA* 1.3 62.3 + - - +
71F HIS* 3.3 4.6 - - - +
72F ALA 3.3 8.3 + - - -
81F ASP* 3.8 20.4 - - - +
84F LEU* 3.6 36.6 - - + -
85F LEU* 3.9 21.3 - - + -
87F ARG* 3.9 13.9 - - - -
68H PHE* 4.0 18.4 - + - -
71H HIS* 3.0 30.4 + - + +
84H LEU* 4.2 17.7 - - + -
87H ARG* 3.8 35.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU 3.0 14.3 + - - +
66F GLU* 3.7 5.4 - - - +
68F PHE* 1.3 75.2 - - - +
70F ARG* 1.3 60.5 + - - +
72F ALA* 3.1 10.4 + - - -
74F ARG* 2.9 50.7 + - - +
75F THR* 5.0 2.0 - - - -
76F THR 4.3 2.2 - - - +
77F ILE* 3.9 15.9 - - + +
81F ASP* 3.4 18.5 + - - +
28G THR* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F GLU* 3.0 17.5 + - + +
67F MET* 3.8 6.5 - - - +
69F ALA* 1.3 76.3 - - - +
71F HIS* 1.3 58.2 + - - +
73F LYS* 2.9 19.6 + - - +
74F ARG 3.3 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F MET 2.9 13.4 + - - +
68F PHE* 3.3 15.0 - - - +
70F ARG* 1.3 78.1 - - - +
72F ALA* 1.3 56.0 + - - +
73F LYS* 3.5 2.6 + - - +
68H PHE* 3.0 25.6 + + + +
71H HIS* 4.5 9.4 - + + -
72H ALA* 3.9 14.5 - - + +
74H ARG* 3.7 12.0 + - - -
80H GLU* 4.1 23.7 + - + +
81H ASP* 2.9 28.7 + - - -
84H LEU* 3.7 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE 3.3 1.2 + - - -
69F ALA 3.1 4.6 + - - +
71F HIS* 1.3 75.0 - - - +
73F LYS* 1.3 68.4 + - - +
74F ARG* 3.2 41.8 + - - +
71H HIS* 3.7 28.9 - - + +
72H ALA* 4.7 5.4 - - - +
----------------------------------------------------------
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