Contacts of the helix formed by residues 10 - 38 (chain O) in PDB entry 1MFR
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 10 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O ARG* 4.0 4.2 + - - +
8O TYR 3.7 1.6 + - - -
9O HIS* 1.3 84.0 + - - +
11O ASP* 1.3 64.9 + - - +
13O GLU* 3.4 18.5 + - - +
14O ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O HIS* 2.8 23.6 + - - +
10O SER* 1.3 73.5 - - - +
12O CYS* 1.3 62.6 + - - +
14O ALA* 3.4 6.7 + - - +
15O ALA* 2.9 29.3 + - - +
18O ARG* 4.6 2.1 + - - -
116O LEU* 3.6 22.1 - - + +
120O LYS* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 12 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O TYR* 4.1 10.3 - - + -
9O HIS* 3.1 25.7 + - + +
11O ASP* 1.3 79.7 - - - +
13O GLU* 1.3 57.0 - - - +
15O ALA* 3.1 3.2 + - - +
16O VAL* 2.9 36.4 + - - +
113O LEU* 4.3 1.2 - - - +
116O LEU* 4.0 25.4 - - - -
117O ALA* 4.3 8.1 - - - -
120O LYS* 4.1 15.7 - - - -
122O ASP* 5.0 4.9 - - - -
125O LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O ARG* 2.7 34.7 + - - -
8O TYR* 3.7 20.8 + - + -
9O HIS 3.1 8.7 + - - +
10O SER* 3.5 18.2 + - - +
12O CYS* 1.3 79.5 - - - +
14O ALA* 1.3 62.2 + - - +
16O VAL 3.3 0.7 + - - -
17O ASN* 3.1 21.8 + - - +
69O GLN* 3.2 27.5 + - - +
74O GLY* 3.8 2.5 - - - -
75O ARG* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O SER 3.1 16.3 + - - +
11O ASP* 3.7 7.9 - - - +
12O CYS 3.3 0.2 - - - -
13O GLU* 1.3 78.9 - - - +
15O ALA* 1.3 62.1 + - - +
17O ASN* 3.5 9.9 + - - +
18O ARG* 3.1 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ASP 2.9 18.2 + - - +
12O CYS 3.1 1.3 + - - +
14O ALA* 1.3 74.7 - - - +
16O VAL* 1.3 60.6 + - - +
18O ARG* 3.3 23.4 + - - +
19O MET* 2.9 29.1 + - - +
113O LEU* 3.5 28.3 - - + +
116O LEU* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O TYR* 3.6 15.3 - - - +
12O CYS 2.9 19.5 + - - +
13O GLU 3.6 4.9 - - - +
15O ALA* 1.3 76.2 - - - +
17O ASN* 1.3 56.9 + - - +
19O MET* 3.2 7.1 + - - +
20O LEU* 2.9 29.5 + - + +
65O PHE* 3.9 34.1 - - + +
68O TYR* 4.6 5.2 - - + -
69O GLN* 3.5 21.3 - - + +
113O LEU* 4.3 12.1 - - + -
125O LEU* 4.3 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O GLU* 3.1 15.8 + - - +
14O ALA* 3.6 12.4 - - - +
15O ALA 3.3 0.2 - - - -
16O VAL* 1.3 76.2 - - - +
18O ARG* 1.3 62.0 + - - +
20O LEU* 3.5 17.9 - - - +
21O ASN* 3.4 19.2 + - - +
69O GLN* 3.4 12.7 + - - +
75O ARG 3.2 19.2 + - - -
76O VAL* 3.3 10.2 - - - -
77O VAL* 3.1 46.6 + - + +
79O GLN* 4.6 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ASP 4.6 2.6 + - - -
14O ALA* 3.1 20.5 + - - +
15O ALA* 3.4 34.1 - - - +
17O ASN* 1.3 79.1 - - - +
19O MET* 1.3 65.2 + - - +
21O ASN* 3.4 6.9 + - - +
22O LEU* 3.1 20.6 + - - +
79O GLN* 4.8 16.4 - - - +
116O LEU* 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 19 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O ALA 2.9 17.0 + - - +
16O VAL* 3.2 6.3 + - - +
18O ARG* 1.3 75.2 - - - +
20O LEU* 1.3 64.5 + - - +
22O LEU* 3.2 14.1 + - - +
23O GLU* 2.9 27.5 + - + +
65O PHE* 3.4 30.5 - - + -
106O VAL* 4.6 3.1 - - - +
109O ALA* 3.1 50.9 - - + +
110O LEU* 3.5 21.1 - - + +
113O LEU* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 5.2 0.2 - - - +
16O VAL* 2.9 16.2 + - + +
17O ASN* 3.5 19.5 - - - +
19O MET* 1.3 77.6 - - - +
21O ASN* 1.3 63.5 + - + +
23O GLU* 3.4 8.3 + - - +
24O LEU* 3.1 42.1 + - + +
62O ALA* 3.7 15.9 - - - +
65O PHE* 4.2 13.6 - - + +
66O MET* 3.8 35.2 - - + +
69O GLN* 5.8 0.7 - - + +
76O VAL* 4.0 18.8 - - + -
77O VAL 5.6 0.4 - - - +
78O LEU* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 4.4 2.4 + - - +
17O ASN 3.4 7.2 + - - +
18O ARG 3.6 9.0 - - - +
19O MET 3.2 0.4 - - - -
20O LEU* 1.3 82.7 - - + +
22O LEU* 1.3 61.1 + - - +
24O LEU* 3.1 8.6 + - - +
25O TYR* 2.8 29.8 + - - +
79O GLN* 3.5 42.4 + - - +
80O ASP 3.2 28.3 + - - +
81O ILE* 4.3 9.7 - - - +
82O LYS 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ARG 3.1 14.6 + - - +
19O MET* 3.2 15.7 + - - +
21O ASN* 1.3 78.3 + - - +
23O GLU* 1.3 58.0 + - - +
25O TYR* 3.2 24.1 + - + +
26O ALA* 2.9 26.3 + - - +
102O LEU* 5.4 1.3 - - + -
105O THR* 4.4 16.2 - - + +
106O VAL* 3.9 30.7 - - + +
109O ALA* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O MET* 2.9 20.3 + - + +
20O LEU 3.4 9.0 - - - +
21O ASN 3.2 0.2 - - - -
22O LEU* 1.3 75.9 - - - +
24O LEU* 1.3 57.3 + - - +
26O ALA* 3.3 5.6 + - - +
27O SER* 2.9 28.4 + - - -
58O GLU* 2.7 20.4 - - - +
61O HIS* 3.4 18.3 - - + +
62O ALA* 3.8 13.9 - - + +
65O PHE* 4.1 19.7 - - + -
106O VAL* 4.0 15.2 - - - +
110O LEU* 4.9 2.8 - - - +
133O TYR* 3.7 15.6 - - - -
176O MG 2.4 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.6 37.7 - - + +
20O LEU* 3.1 32.1 + - + +
21O ASN* 3.1 9.2 + - - +
23O GLU* 1.3 76.2 - - - +
25O TYR* 1.3 57.2 + - - +
27O SER* 3.5 6.4 - - - +
28O TYR* 3.0 27.5 + - - +
59O ARG* 4.9 17.0 - - + -
62O ALA* 3.7 18.6 - - + -
63O GLU* 6.4 0.4 - - + -
66O MET* 5.1 6.3 - - + -
81O ILE* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O ASN* 2.8 17.6 + - - +
22O LEU* 3.4 28.3 - - + +
24O LEU* 1.3 73.6 - - - +
26O ALA* 1.3 63.2 - - - +
28O TYR* 3.2 4.3 + - + +
29O THR* 2.9 47.7 + - + -
81O ILE* 4.0 10.0 - - + +
82O LYS* 3.4 37.5 - - + +
83O LYS 3.8 11.4 + - - -
84O PRO* 4.1 1.8 - - + -
85O GLU* 3.8 25.5 + - - +
102O LEU* 4.1 17.3 - - + -
105O THR* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O LEU 2.9 14.3 + - - +
23O GLU* 3.3 9.8 + - - +
25O TYR* 1.3 77.3 - - - +
27O SER* 1.3 62.1 + - - +
29O THR* 3.3 2.8 + - - -
30O TYR* 3.1 31.1 + - + -
58O GLU* 4.2 15.0 - - + -
102O LEU* 3.9 26.6 - - + +
103O GLU* 6.5 0.7 - - - -
106O VAL* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU 2.9 16.9 + - - -
24O LEU* 3.5 11.2 - - - +
26O ALA* 1.3 76.8 - - - +
28O TYR* 1.3 62.5 + - - +
30O TYR 3.1 2.8 + - - -
31O SER* 3.0 19.0 + - - -
55O SER* 2.9 39.3 + - - +
58O GLU* 3.8 11.8 - - - +
59O ARG* 3.6 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 4.4 2.8 + - - -
24C LEU* 3.6 27.4 - - + +
66C MET* 5.5 0.4 - - + -
78C LEU* 3.3 37.7 - - + +
79C GLN 3.0 30.6 + - - -
81C ILE* 3.8 22.4 - - + +
24O LEU 3.0 18.4 + - - +
25O TYR* 3.2 5.6 + - - +
27O SER* 1.3 77.4 - - - +
29O THR* 1.3 60.0 + - - +
31O SER* 3.2 15.6 - - - -
32O SER* 3.2 18.5 + - - -
81O ILE* 4.0 13.0 - - + -
82O LYS 3.6 17.9 - - - +
83O LYS* 4.0 3.6 - - - -
84O PRO* 3.7 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O TYR* 2.9 31.1 + - + +
26O ALA 3.6 8.1 - - - -
27O SER 3.2 0.2 - - - -
28O TYR* 1.3 75.2 - - - +
30O TYR* 1.3 62.2 + - - +
32O SER* 3.2 6.8 + - - -
33O MET* 3.2 39.4 + - + +
84O PRO* 3.4 20.7 - - - +
85O GLU 5.8 0.2 - - - +
89O TRP* 4.0 15.4 - - + -
102O LEU* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ALA* 3.1 23.6 + - + -
27O SER 3.1 6.5 + - - +
29O THR* 1.3 74.9 - - - +
31O SER* 1.3 59.4 + - - +
33O MET* 3.2 13.4 + - + +
34O TYR* 2.8 28.2 + - - +
50O PHE* 5.9 0.2 - + - -
51O PHE* 3.6 47.1 - + - +
54O HIS* 3.9 28.0 - + + -
55O SER* 3.7 7.4 - - - -
58O GLU* 4.0 13.2 - - + -
99O ALA* 3.9 24.3 + - + +
102O LEU* 3.9 18.3 - - + +
103O GLU* 2.8 41.5 + - - +
144O ILE* 4.3 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 6.1 0.2 - - - +
63C GLU* 4.9 5.9 + - - +
66C MET* 3.3 30.4 - - - +
78C LEU* 4.9 1.1 - - - -
27O SER 3.0 12.9 + - - -
28O TYR* 3.2 24.2 - - - -
30O TYR* 1.3 74.9 - - - +
32O SER* 1.3 61.3 + - - +
34O TYR* 3.4 12.6 + - - +
35O ALA* 3.1 22.5 + - - +
55O SER* 3.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 6.4 0.2 - - - -
78C LEU* 3.4 16.7 - - - +
28O TYR 3.2 5.3 + - - -
29O THR 3.2 11.4 + - - -
30O TYR 3.2 0.6 - - - -
31O SER* 1.3 73.1 - - - +
33O MET* 1.3 60.3 + - - +
35O ALA* 3.2 7.8 + - - +
36O PHE* 2.9 28.1 + - - +
84O PRO* 3.2 29.1 - - - +
86O ARG 4.0 6.8 + - - -
87O ASP* 5.1 7.3 + - - +
89O TRP* 3.4 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O THR* 3.2 32.6 + - + +
30O TYR* 3.2 15.2 + - + +
32O SER* 1.3 76.5 - - - +
34O TYR* 1.3 65.5 + - - +
36O PHE* 3.3 1.1 + - - +
37O PHE* 3.0 32.8 + - + -
51O PHE* 3.8 43.1 - - + -
89O TRP* 3.7 43.7 - - + +
95O ALA* 3.8 22.9 - - + +
98O ALA* 4.0 7.9 - - + +
99O ALA* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 5.1 11.2 - - + -
66C MET* 4.5 22.9 - - + -
67C LYS* 3.3 38.1 - - + +
70C ASN* 6.3 0.2 - - - -
30O TYR 2.8 13.7 + - - +
31O SER* 3.4 15.0 - - - +
33O MET* 1.3 76.7 - - - +
35O ALA* 1.3 71.5 + - - +
37O PHE 3.4 0.5 + - - -
38O ASP* 3.2 29.8 + - + +
48O ALA* 3.2 38.7 - - + +
49O GLU* 3.6 19.5 + - - -
51O PHE* 4.0 2.6 - - - +
52O LYS* 3.7 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C MET* 4.3 14.4 - - + -
70C ASN* 3.1 27.2 + - - +
76C VAL* 4.2 31.9 - - + -
31O SER 3.1 10.2 + - - +
32O SER* 3.6 9.2 - - - +
34O TYR* 1.3 86.2 - - + +
36O PHE* 1.3 62.5 + - - +
38O ASP* 4.4 0.9 - - - -
39O ARG* 3.5 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O SER 2.9 17.0 + - - +
33O MET 3.5 4.9 - - - +
34O TYR 3.1 0.4 - - - -
35O ALA* 1.3 77.9 - - - +
37O PHE* 1.3 85.5 + + - +
39O ARG* 3.3 52.5 - - - +
42O VAL* 3.3 34.9 - - + +
87O ASP 4.5 4.0 - - - +
88O GLU* 3.8 11.7 - - + -
89O TRP* 3.6 32.1 - - + -
90O GLY* 3.5 40.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O MET* 3.0 27.2 + - + +
34O TYR 3.4 0.2 + - - -
36O PHE* 1.3 91.7 - + - +
38O ASP* 1.3 60.2 + - - +
39O ARG 3.2 0.4 - - - -
42O VAL* 3.5 23.3 - - + -
43O ALA* 3.5 7.3 + - - -
44O LEU* 3.2 51.2 + - + +
45O HIS* 4.3 0.9 + - - -
47O VAL* 3.9 10.8 - - + -
48O ALA* 3.7 14.1 - - + -
51O PHE* 3.7 19.5 - + - -
89O TRP* 4.8 0.4 - - + -
91O ASN* 3.5 24.2 - - - -
92O THR* 3.6 27.4 - - - -
95O ALA* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.2 44.7 + - - +
70C ASN* 3.1 30.9 + - - +
34O TYR* 3.2 28.8 + - + +
35O ALA* 4.3 1.3 - - - -
36O PHE 3.2 0.4 - - - -
37O PHE* 1.3 74.2 - - - +
39O ARG* 1.3 61.2 + - - +
45O HIS* 3.4 23.0 + - - -
48O ALA* 4.1 2.5 - - + +
142R LYS* 2.9 30.9 + - - -
----------------------------------------------------------
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