Contacts of the helix formed by residues 42 - 70 (chain A) in PDB entry 1NF6
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 TYR 42 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.0 13.8 + - + +
40A MET* 3.8 42.6 - - + -
41A ASP* 1.3 73.5 - - - +
43A GLY* 1.3 62.1 - - - +
44A GLU 3.4 2.2 - - - -
45A LEU* 3.0 19.0 + - + +
46A ALA* 2.9 20.8 + - - +
88A VAL* 4.4 11.2 - - + -
154A LEU* 3.7 51.3 - - + +
157A ILE* 3.7 17.9 - - + -
158A ALA* 3.7 27.6 - - + -
145N HIS* 4.2 8.4 - + - -
148N ASN* 5.4 5.0 + - - +
149N LEU* 4.3 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 5.1 1.6 - - - -
41A ASP* 3.4 8.4 + - - -
42A TYR* 1.3 72.2 - - - +
44A GLU* 1.3 56.0 + - - +
46A ALA* 3.1 5.5 + - - +
47A ALA* 2.8 29.8 + - - +
160A THR* 3.2 25.3 + - - -
161A PRO 3.2 8.7 - - - -
162A SER* 3.5 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR 3.4 0.2 - - - -
43A GLY* 1.3 71.8 - - - +
45A LEU* 1.3 65.7 + - - +
47A ALA* 3.7 5.2 - - + +
48A ASN* 3.1 46.1 + - - +
153A TYR* 5.1 2.2 + - - -
156A LYS* 5.6 1.7 - - - -
157A ILE* 3.6 26.7 - - + +
160A THR* 3.0 25.7 + - + +
161A PRO 3.4 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 15.2 - - + +
42A TYR* 3.0 23.8 + - + +
44A GLU* 1.3 80.4 - - + +
46A ALA* 1.3 62.9 + - - +
48A ASN* 4.2 1.4 - - - +
49A MET* 3.1 25.6 + - - +
88A VAL* 4.6 5.2 - - + -
92A TYR* 3.4 33.0 + - + +
138A TYR* 3.9 13.3 + - - +
142A ILE* 3.9 22.0 - - + -
146A ILE* 5.3 0.2 - - + -
153A TYR* 4.1 15.9 - - + +
154A LEU* 4.3 20.6 - - + -
157A ILE* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 2.6 36.4 + - + +
37A LEU* 3.9 9.8 - - + +
38A ASP* 3.6 41.5 - - + +
42A TYR 2.9 10.5 + - - +
43A GLY* 3.1 9.2 + - - +
45A LEU* 1.3 77.6 - - - +
47A ALA* 1.3 60.8 + - - +
49A MET* 3.5 1.0 + - - +
50A LYS 3.1 11.4 + - - -
162A SER* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 5.1 0.2 - - - -
43A GLY 2.8 16.4 + - - +
44A GLU* 3.7 9.6 - - + +
46A ALA* 1.3 74.2 - - - +
48A ASN* 1.3 62.7 + - - +
50A LYS 3.3 1.7 + - - -
51A LEU* 3.0 35.1 + - + +
161A PRO 4.6 1.6 - - - +
162A SER* 3.5 23.5 + - - +
163A SER 3.9 13.7 - - - +
164A THR* 3.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.1 38.4 + - - +
45A LEU 4.2 0.2 - - - +
47A ALA* 1.3 80.5 - - - +
49A MET* 1.3 56.6 + - - +
51A LEU* 3.3 15.6 + - - +
52A ILE* 2.9 35.6 + - - +
138A TYR* 3.2 38.3 + - + +
171B PHE* 3.8 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.3 28.9 - - - +
33A GLN* 3.5 16.8 - - + +
34A HIS* 3.9 11.9 - - + +
37A LEU* 3.8 14.6 - - + -
45A LEU 3.1 17.3 + - - +
46A ALA 3.7 4.7 - - - +
47A ALA 3.3 0.2 - - - -
48A ASN* 1.3 76.7 - - - +
50A LYS* 1.3 57.0 + - - +
52A ILE* 3.3 4.6 + - - +
53A ALA* 3.0 26.6 + - - +
91A ILE* 3.6 22.4 - - + -
92A TYR* 3.9 9.4 - - + +
95A ASP* 3.5 14.6 - - - +
138A TYR* 5.0 1.3 + - + -
139A TYR* 3.4 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 3.8 24.2 - - + -
34A HIS* 3.6 21.5 + - + +
46A ALA 3.1 15.5 + - - +
47A ALA 3.6 4.5 - - - +
49A MET* 1.3 77.7 - - - +
51A LEU* 1.3 59.2 + - - +
53A ALA* 3.2 3.3 + - - +
54A ILE* 3.0 34.4 + - + +
164A THR* 3.7 13.4 + - + -
1001A SO4 2.7 35.0 + - - +
1005A FEC 3.6 30.6 - - - +
61B GLU* 2.7 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.0 24.2 + - + +
48A ASN* 3.3 19.9 + - - +
50A LYS* 1.3 75.7 - - - +
52A ILE* 1.3 61.9 + - - +
54A ILE* 3.5 7.3 + - + +
55A ASP* 3.2 13.3 + - - +
164A THR* 3.9 36.6 - - + +
169B LYS* 3.2 31.6 - - + +
170B GLY* 3.6 10.5 - - - +
171B PHE* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 4.2 5.6 - - + -
48A ASN 2.9 19.3 + - - +
49A MET 3.8 3.8 - - - +
51A LEU* 1.3 73.3 - - - +
53A ALA* 1.3 66.5 + - - +
55A ASP* 3.1 5.6 + - - +
56A GLU* 3.0 32.9 + - - +
135A HIS* 3.6 32.5 - - + +
138A TYR* 3.5 35.2 - - + -
139A TYR* 3.5 30.3 - - + +
171B PHE* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.9 7.8 - - - +
30A TYR* 4.0 15.9 - - + -
31A MET* 3.9 30.3 - - + -
49A MET 3.0 13.8 + - - +
50A LYS 3.2 10.0 + - - +
52A ILE* 1.3 77.6 - - - +
54A ILE* 1.3 56.8 + - - +
56A GLU* 3.1 13.2 + - - +
57A MET* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 3.0 32.2 + - + +
51A LEU* 3.7 9.9 - - + +
52A ILE 3.2 0.4 - - - -
53A ALA* 1.3 73.6 - - - +
55A ASP* 1.3 64.1 + - - +
57A MET* 3.4 28.9 + - + +
58A ARG* 3.1 23.0 + - + +
164A THR* 5.5 2.5 - - - +
1005A FEC 3.9 37.9 - - + +
168B SER* 3.8 25.1 - - - +
169B LYS 3.7 24.5 - - - +
170B GLY* 4.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 3.2 4.6 + - - -
52A ILE 3.1 8.8 + - - +
54A ILE* 1.3 77.7 - - - +
56A GLU* 1.3 58.2 - - - +
58A ARG* 3.3 28.3 + - - +
59A HIS* 3.0 34.0 + - - +
135A HIS* 2.8 32.6 + - + -
170B GLY* 2.9 12.6 - - - -
171B PHE* 2.7 40.0 + - - +
172B VAL* 2.9 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.3 24.4 - - - +
26A ALA* 4.2 5.5 - - + +
27A ILE* 3.9 13.8 - - + +
30A TYR* 3.4 25.5 - - + -
52A ILE 3.0 16.6 + - - +
53A ALA* 3.1 6.7 + - - +
55A ASP* 1.3 72.1 - - - +
57A MET* 1.3 60.4 + - - +
59A HIS* 3.1 21.8 + - - +
60A ALA* 2.9 27.0 + - - +
99A GLU* 3.2 11.8 - - - +
132A GLU* 3.3 3.3 - - - +
135A HIS* 3.4 4.2 + - - -
200A FE 2.1 31.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.7 26.9 - - + +
31A MET* 4.6 5.2 - - + -
53A ALA* 2.9 27.9 + - + +
54A ILE* 3.5 27.4 - - + +
55A ASP 3.3 0.2 - - - -
56A GLU* 1.3 74.7 - - - +
58A ARG* 1.3 64.1 + - - +
60A ALA* 3.3 3.6 + - - +
61A GLU* 3.0 22.7 + - - +
1005A FEC 2.4 100.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.1 15.7 + - - +
55A ASP* 3.3 34.6 + - - +
57A MET* 1.3 71.6 - - - +
59A HIS* 1.3 61.3 + - - +
61A GLU* 3.2 13.1 + - - +
62A ASN* 2.8 49.6 + - - +
131A GLU* 3.0 36.7 + - - -
1005A FEC 4.3 12.1 - - + +
167B ALA* 5.6 5.4 - - - -
168B SER* 2.9 35.1 + - - +
170B GLY* 5.0 0.6 - - - -
172B VAL* 3.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.9 30.3 + - + +
55A ASP* 3.0 25.3 + - - +
56A GLU* 3.1 21.1 + - - +
58A ARG* 1.3 81.4 - - - +
60A ALA* 1.3 63.6 + - - +
62A ASN* 3.0 6.2 + - - +
63A PHE* 3.0 28.5 + - - -
128A ILE* 3.6 41.4 - - + +
131A GLU* 2.5 34.8 + - + -
132A GLU* 3.3 21.9 + - - -
135A HIS* 4.3 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.0 31.5 + - + +
23A GLU* 4.0 18.1 - - + +
24A LEU* 4.4 6.3 - - + -
27A ILE* 4.4 11.4 - - + -
56A GLU 2.9 16.2 + - - +
57A MET 3.3 9.6 + - - +
59A HIS* 1.3 73.1 - - - +
61A GLU* 1.3 56.7 + - - +
63A PHE* 3.4 7.1 + - - +
64A ALA 2.9 23.7 + - - -
1005A FEC 4.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 3.0 11.5 + - - +
58A ARG* 3.3 14.3 - - - +
60A ALA* 1.3 73.2 - - - +
62A ASN* 1.3 70.6 + - - +
64A ALA* 3.2 2.1 + - - +
65A GLU* 2.9 50.0 + - - +
1005A FEC 2.8 40.0 - - + +
31B MET* 4.5 1.3 - - - +
34B HIS* 4.1 6.9 + - - -
35B TYR* 3.5 19.9 + - + +
50B LYS* 2.6 34.3 + - - +
1201B SO4 4.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 2.8 41.3 + - - +
59A HIS* 3.7 7.7 - - - +
61A GLU* 1.3 78.0 - - - +
63A PHE* 1.3 58.3 + - - +
65A GLU* 3.3 20.9 + - - +
66A ARG* 3.0 28.2 + - - +
124A LEU* 3.8 29.5 - - + +
128A ILE* 4.6 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.6 26.9 - - + +
19A ALA* 3.9 13.9 - - + -
20A ARG* 4.0 23.1 - - + -
23A GLU* 3.8 16.4 - - + -
59A HIS 3.0 20.3 + - - -
60A ALA 3.5 6.1 - - - +
62A ASN* 1.3 74.4 - - - +
64A ALA* 1.3 59.3 + - - +
66A ARG* 3.3 3.3 + - - +
67A ILE* 2.9 34.6 + - - +
106A TYR* 3.7 28.3 - + - -
124A LEU* 3.9 13.5 - - + -
125A PHE* 3.9 28.0 - + - -
128A ILE* 3.3 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.7 6.7 - - - +
60A ALA 2.9 17.4 + - - +
61A GLU 3.2 1.1 + - - +
63A PHE* 1.3 76.0 - - - +
65A GLU* 1.3 57.5 + - - +
67A ILE* 3.4 2.0 + - - -
68A LYS* 3.0 34.4 + - - +
74A PRO* 3.6 31.7 - - + +
35B TYR* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.9 39.3 + - + +
62A ASN* 3.6 26.7 + - - +
63A PHE 3.2 0.2 - - - -
64A ALA* 1.3 78.5 - - - +
66A ARG* 1.3 56.7 + - - +
68A LYS* 3.4 8.1 + - - +
69A GLU* 3.0 34.9 + - - +
34B HIS* 4.7 4.3 + - - -
35B TYR* 4.4 12.6 - - + -
38B ASP* 4.2 15.7 - - + +
1201B SO4 5.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.0 12.3 - - + -
62A ASN 3.0 16.7 + - - +
63A PHE 3.8 3.8 - - - +
65A GLU* 1.3 72.7 - - - +
67A ILE* 1.3 67.1 + - - +
69A GLU* 3.0 46.7 + - - +
70A LEU* 3.0 30.1 + - - +
118A ASP* 2.8 32.7 + - - -
120A VAL* 3.6 26.1 - - - +
121A THR* 2.7 31.7 + - + +
124A LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.3 11.7 - - + +
16A LEU* 3.6 39.5 - - + +
17A ASN* 3.3 29.8 - - - +
20A ARG* 4.2 4.7 - - - -
63A PHE 2.9 23.9 + - - +
64A ALA* 3.7 4.0 - - - +
65A GLU 3.3 0.2 - - - -
66A ARG* 1.3 76.2 - - - +
68A LYS* 1.3 64.6 + - - +
70A LEU* 3.0 11.7 + - - +
71A GLY 3.2 0.2 + - - -
72A GLY* 2.9 49.1 + - - +
73A GLU 3.6 2.9 - - - +
74A PRO* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 3.0 21.8 + - - +
65A GLU* 3.6 7.2 - - - +
67A ILE* 1.3 76.6 - - - +
69A GLU* 1.3 63.0 + - + +
71A GLY* 3.1 13.7 + - - -
72A GLY 3.4 17.4 + - - +
73A GLU* 3.6 22.4 + - - -
74A PRO* 3.7 14.1 - - + +
32B ASN 5.1 0.4 + - - -
35B TYR* 3.5 36.0 - - + +
36B SER* 3.1 26.0 + - - +
39B ASP* 3.9 35.6 + - + +
85B GLY* 6.1 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 5.1 3.1 - - - -
65A GLU* 3.0 21.6 + - - +
66A ARG* 3.0 44.8 + - - +
68A LYS* 1.3 76.9 - - + +
70A LEU* 1.3 61.6 + - - +
71A GLY 3.6 0.5 + - - -
120A VAL* 4.9 4.5 - - - +
39B ASP* 5.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 3.4 52.9 - - + +
12A VAL* 3.8 17.0 - - + -
13A ILE* 3.7 24.5 - - + +
16A LEU* 3.6 30.5 - - + -
66A ARG* 3.0 28.6 + - - +
67A ILE 3.0 8.2 + - - +
69A GLU* 1.3 78.9 - - - +
71A GLY* 1.3 60.1 + - - +
118A ASP* 3.8 13.9 - - - +
121A THR* 3.8 9.2 - - - +
----------------------------------------------------------
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