Contacts of the helix formed by residues 38 - 67 (chain S) in PDB entry 2BKC
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 ASN 38 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS* 3.3 49.7 + - - +
38P ASN* 5.0 5.7 - - - +
41P THR* 5.2 1.0 - - - +
36S GLY 3.0 1.6 + - - -
37S HIS* 1.3 83.8 + - - +
39S PHE* 1.3 62.0 + - - +
40S PHE 3.3 2.7 - - - -
41S THR* 3.4 19.8 + - - +
42S LEU* 3.1 36.1 + - + +
95S MET* 4.1 15.2 - - + +
149S PHE* 3.9 13.8 - - + -
38U ASN* 5.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S HIS* 4.6 6.7 - + - -
32S TRP 5.4 0.2 - - - -
34S MET* 3.4 38.7 - - + +
35S ARG 5.0 0.2 - - - -
36S GLY 3.0 18.2 + - - +
37S HIS 3.3 1.8 + - - -
38S ASN* 1.3 77.4 - - - +
40S PHE* 1.3 73.2 + + + +
43S GLY* 3.0 29.2 + - - -
95S MET* 4.2 9.2 - - - +
144U TRP* 4.0 25.8 - + - -
145U MET* 3.6 52.3 - - + -
148U ALA* 3.7 17.3 - - + -
149U PHE* 4.2 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S HIS 4.8 1.3 + - - -
38S ASN 3.3 0.6 - - - -
39S PHE* 1.3 87.3 - + - +
41S THR* 1.3 63.9 + - + +
43S GLY* 4.1 0.2 - - - -
44S GLU* 3.3 33.7 + - - +
41U THR* 3.9 13.5 - - - +
42U LEU* 4.0 19.5 - - + -
45U LYS* 3.6 42.4 - - + -
145U MET* 4.0 34.3 - - + -
146U PHE* 3.6 43.7 - + - -
149U PHE* 4.0 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS 5.5 0.8 + - - +
40P PHE* 3.9 21.0 - - - +
41P THR* 3.8 24.0 - - + +
37S HIS 5.0 1.6 - - - +
38S ASN* 3.7 33.0 - - - +
40S PHE* 1.3 80.9 - - - +
42S LEU* 1.3 66.5 + - + +
44S GLU* 3.5 10.5 + - - +
45S LYS* 3.1 26.5 + - - +
41U THR* 4.4 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P HIS 5.4 0.4 - - - +
40P PHE* 4.4 10.5 - - + -
34S MET* 4.0 15.3 - - + -
38S ASN* 3.1 21.2 + - + +
41S THR* 1.3 87.4 - - + +
43S GLY* 1.3 58.1 + - - +
45S LYS* 3.7 5.3 - - + +
46S MET* 2.7 41.4 + - + +
95S MET* 3.4 25.1 - - + -
99S MET* 3.6 25.6 - - - -
146S PHE* 5.0 10.3 - - + -
149S PHE* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S HIS* 3.1 41.5 + - - -
34S MET* 3.6 8.6 - - - -
39S PHE* 3.0 22.9 + - - -
40S PHE* 4.1 0.7 - - - -
42S LEU* 1.3 78.3 - - - +
44S GLU* 1.3 60.2 + - - +
47S ASP* 3.1 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S PHE* 3.3 22.6 + - - +
41S THR* 3.5 11.7 - - - +
42S LEU 3.3 0.2 - - - -
43S GLY* 1.3 75.6 - - - +
45S LYS* 1.3 59.6 + - + +
47S ASP* 3.2 26.3 - - - +
48S ASP* 3.2 16.3 + - - +
45U LYS* 4.6 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P PHE* 3.4 50.0 - - + -
44P GLU* 5.3 7.6 - - - +
41S THR 3.1 19.3 + - - +
42S LEU* 3.2 9.6 + - + +
44S GLU* 1.3 73.9 - - + +
46S MET* 1.3 63.3 + - + +
48S ASP* 3.5 20.8 + - + +
49S LEU* 3.1 32.9 + - - +
141S LYS* 5.7 1.3 - - - +
142S HIS* 4.2 10.5 + - - -
145S MET* 4.1 16.5 - - - +
146S PHE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S ILE* 3.2 31.7 - - + +
30S ILE* 3.8 23.1 - - + -
31S HIS* 3.8 16.6 - - + +
34S MET* 3.5 21.1 - - + -
42S LEU* 2.7 28.6 + - + +
43S GLY 3.7 4.0 - - - +
45S LYS* 1.3 73.7 - - + +
47S ASP* 1.3 60.2 + - - +
49S LEU* 4.4 5.8 - - + -
50S TYR* 2.9 25.5 + - - +
99S MET* 4.3 7.6 - - + -
102S LEU* 4.1 19.7 - - + -
146S PHE* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ASP* 5.7 2.3 - - - +
28S HIS* 5.7 4.5 - - - -
31S HIS* 3.4 23.1 + - - -
43S GLY 3.1 15.4 + - - +
44S GLU* 3.2 17.1 - - - +
46S MET* 1.3 76.2 - - - +
48S ASP* 1.3 63.9 + - - +
50S TYR* 3.4 7.2 + - - +
51S SER* 3.2 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S GLU* 3.2 15.6 + - - +
45S LYS* 3.7 23.4 - - + +
47S ASP* 1.3 76.9 - - - +
49S LEU* 1.3 63.1 + - + +
51S SER* 3.6 5.6 + - - -
52S GLU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S PHE* 4.4 4.0 - - + -
27S ILE* 3.9 19.4 - - + +
45S LYS* 3.1 21.4 + - - +
46S MET* 3.4 10.7 + - + +
48S ASP* 1.3 76.3 - - + +
50S TYR* 1.3 61.3 + - - +
52S GLU* 4.2 3.6 - - - +
53S PHE* 2.9 58.3 + - + +
102S LEU* 4.0 31.4 - - + -
106S LEU* 4.9 5.2 - - + -
142S HIS* 3.4 39.3 - - + +
146S PHE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASN* 5.6 0.9 + - - -
24Q THR* 5.7 4.5 - - - +
50Q TYR* 4.7 12.4 + + - -
54Q GLY* 5.9 3.3 - - - -
57Q MET* 4.6 6.2 - - - +
58Q ASP* 5.4 2.2 - - - -
24S THR* 3.4 49.9 + - + +
27S ILE* 3.9 12.7 - - + +
28S HIS* 3.2 49.0 + + + +
46S MET 2.9 19.1 + - - +
47S ASP* 3.5 8.5 - - - +
48S ASP 3.3 0.2 - - - -
49S LEU* 1.3 77.5 - - - +
51S SER* 1.3 65.4 + - - +
54S GLY* 3.0 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S ASP 3.2 14.5 + - - -
48S ASP* 3.9 5.6 - - - -
50S TYR* 1.3 83.4 - - - +
52S GLU* 1.3 64.6 + - - +
54S GLY* 3.9 1.0 - - - -
55S GLU* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S ASP* 2.9 19.1 + - - +
49S LEU* 3.8 6.8 - - - +
51S SER* 1.3 75.9 - - - +
53S PHE* 1.3 71.0 + - + +
55S GLU* 3.2 16.9 + - + +
56S GLN* 3.1 30.3 + - + +
138S SER* 2.5 31.3 + - - -
142S HIS* 2.7 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S LEU* 3.9 19.7 - - + +
23S PHE* 3.9 28.9 - + + -
24S THR* 4.3 8.1 + - - +
27S ILE* 4.6 5.6 - - + -
49S LEU* 2.9 53.1 + - + +
50S TYR 4.5 1.3 - - - +
52S GLU* 1.3 90.8 - - + +
54S GLY* 1.3 64.0 + - - +
55S GLU 3.2 0.2 - - - -
56S GLN* 3.6 38.9 - - - +
57S MET* 3.1 21.8 + - - +
106S LEU* 4.1 16.6 - - + -
109S LEU* 4.8 1.6 - - + -
138S SER* 5.4 0.2 - - - -
139S ILE* 4.2 19.7 - - + -
142S HIS* 4.2 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 5.6 1.2 + - - -
50Q TYR* 5.7 4.9 - - - -
24S THR* 4.0 9.6 + - - -
50S TYR* 3.0 19.6 + - - -
51S SER* 3.9 1.8 - - - -
53S PHE* 1.3 75.9 - - - +
55S GLU* 1.3 63.1 + - - +
57S MET* 3.4 13.3 + - - +
58S ASP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S SER* 3.0 32.9 + - - +
52S GLU* 3.2 17.2 + - - +
54S GLY* 1.3 76.7 - - - +
56S GLN* 1.4 60.2 + - - +
58S ASP* 3.3 8.1 + - - +
59S GLU* 3.2 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S LEU* 4.1 6.0 - - + +
52S GLU* 3.1 25.6 + - + +
53S PHE* 3.4 42.5 + - + +
55S GLU* 1.4 71.5 - - - +
57S MET* 1.3 65.5 + - - +
59S GLU* 3.3 2.5 + - - +
60S VAL* 2.9 29.0 + - - +
113S TYR* 2.7 31.0 + - - -
135S PHE* 3.3 63.5 + - + +
138S SER* 4.7 2.2 - - - -
139S ILE* 4.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 3.6 31.2 - - + +
32Q TRP* 3.6 28.9 - - + -
50Q TYR* 4.6 6.3 - - - +
17S VAL* 4.2 9.9 - - - +
20S LEU* 3.8 27.1 - - + -
21S ASN* 3.5 37.0 - - - +
24S THR* 6.0 2.2 - - + +
53S PHE 3.1 11.8 + - - +
54S GLY* 3.5 14.1 - - - +
55S GLU 3.2 0.4 - - - -
56S GLN* 1.3 76.4 - - - +
58S ASP* 1.3 67.6 + - - +
60S VAL* 3.1 5.8 + - - +
61S ALA* 2.9 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 3.3 32.2 + - - -
31Q HIS* 4.7 6.1 + - - -
32Q TRP* 3.7 14.9 + - - -
47Q ASP* 5.1 4.3 - - - +
54S GLY 3.1 10.8 + - - +
55S GLU* 3.7 9.9 - - - +
56S GLN 3.3 0.2 - - - -
57S MET* 1.3 83.6 - - - +
59S GLU* 1.3 57.7 + - + +
61S ALA* 3.6 3.3 + - - +
62S GLU* 2.9 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S GLU* 3.2 31.5 + - - +
56S GLN* 3.9 5.2 - - - +
57S MET 3.2 0.4 - - - -
58S ASP* 1.3 73.7 - - + +
60S VAL* 1.3 61.2 + - - +
62S GLU* 3.9 10.0 - - - +
63S ARG* 2.7 33.1 + - - +
131S MET* 4.0 11.5 - - + +
135S PHE* 3.6 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 3.2 42.7 - - + +
16S GLN* 4.4 6.3 - - + -
17S VAL* 3.5 17.3 - - + +
20S LEU* 4.5 11.7 - - + -
56S GLN 2.9 18.4 + - - +
57S MET* 3.5 9.6 - - - +
59S GLU* 1.3 76.6 - - - +
61S ALA* 1.3 58.8 + - - +
63S ARG* 3.1 5.3 + - - +
64S LEU* 2.8 28.1 + - - +
113S TYR* 5.0 1.1 - - + +
131S MET* 4.3 10.5 - - + -
132S LEU* 5.3 2.7 - - + -
135S PHE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q TRP* 3.4 46.0 - - + +
17S VAL* 4.3 14.1 - - + -
57S MET 2.9 12.5 + - - +
58S ASP 3.9 2.9 - - - +
60S VAL* 1.3 76.7 - - - +
62S GLU* 1.3 57.0 + - - +
64S LEU* 3.4 6.9 + - - +
65S LEU* 3.0 33.7 + - - +
71S PRO* 4.4 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q HIS* 4.1 14.2 + - - -
32Q TRP* 4.9 6.3 - - + +
58S ASP* 2.9 47.1 + - - +
59S GLU* 3.9 9.3 - - - +
61S ALA* 1.3 76.5 - - - +
63S ARG* 1.3 59.7 + - - +
65S LEU* 3.3 12.1 + - + +
66S ALA* 2.9 28.6 + - - +
141Y LYS* 3.9 30.0 + - + +
144Y TRP* 4.0 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 4.6 3.1 - - + -
59S GLU 2.7 22.7 + - - +
60S VAL 3.5 3.1 - - - +
62S GLU* 1.3 71.4 - - - +
64S LEU* 1.3 65.1 + - - +
66S ALA* 2.9 18.3 + - - +
67S ILE* 3.1 40.0 + - + +
125S ASP* 2.8 27.1 + - - -
127S VAL* 3.1 35.7 - - + +
128S THR* 2.9 24.9 + - + +
131S MET* 3.9 25.4 - - + -
136Y LYS* 4.3 5.3 - - - +
137Y ALA 6.0 0.9 - - - -
140Y ASP* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S LYS* 3.2 45.8 - - + +
13S LEU* 4.0 13.6 - - + +
14S ASN* 3.2 46.0 - - - +
17S VAL* 4.8 3.4 - - + -
60S VAL 2.8 19.0 + - - +
61S ALA* 3.4 6.3 + - - +
63S ARG* 1.3 71.6 - - - +
65S LEU* 1.3 60.4 + - - +
67S ILE* 3.2 16.0 - - + +
69S GLY* 2.8 35.6 + - - -
70S SER 4.3 2.5 - - - +
71S PRO* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q TRP* 3.7 43.5 - - + +
33Q TYR* 5.0 5.2 - - + -
61S ALA 3.0 18.6 + - - +
62S GLU* 3.4 12.8 - - - +
63S ARG 3.1 0.2 - - - -
64S LEU* 1.3 77.6 - - - +
66S ALA* 1.3 63.5 + - - +
67S ILE 3.4 0.3 + - - -
68S GLY* 3.4 5.7 + - - -
69S GLY 3.7 12.7 + - - +
70S SER* 4.8 0.2 - - - -
71S PRO* 3.3 30.7 - - + -
144Y TRP* 3.8 36.3 - - + +
154Y PRO* 3.1 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62S GLU 2.9 15.8 + - - +
63S ARG* 2.9 26.0 + - - +
65S LEU* 1.3 79.5 - - - +
67S ILE* 1.3 58.5 + - - +
68S GLY 3.4 0.9 + - - -
140Y ASP* 3.8 28.8 - - + +
141Y LYS* 4.6 5.2 - - + +
144Y TRP* 4.0 13.9 - - + -
154Y PRO* 3.8 12.5 - - - +
155Y LEU* 4.1 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S THR* 3.7 30.1 - - + -
10S LYS* 3.7 29.7 - - + -
13S LEU* 3.8 19.7 - - + -
63S ARG* 3.3 47.3 - - - +
64S LEU* 3.2 16.4 - - + +
66S ALA* 1.3 77.4 - - - +
68S GLY* 1.3 55.4 + - - +
125S ASP* 4.3 5.6 - - - +
128S THR* 4.6 0.4 - - - +
155Y LEU* 3.8 20.5 - - + +
----------------------------------------------------------
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