Contacts of the helix formed by residues 38 - 67 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M GLY 3.1 2.4 + - - -
37M HIS* 1.3 85.7 + - - +
39M PHE* 1.3 63.9 - - - +
40M PHE 3.4 2.5 - - - -
41M THR* 3.6 14.1 + - + +
42M LEU* 3.0 37.2 + - + +
95M MET* 3.6 20.3 - - + +
149M PHE* 3.9 11.4 - - + -
38T ASN* 5.0 4.9 - - - +
37X HIS* 3.0 57.2 + - - +
38X ASN* 5.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M HIS* 4.3 11.7 - + - -
32M TRP 5.4 0.4 - - - -
34M MET* 3.4 45.6 - - + +
36M GLY 3.2 16.1 + - - +
37M HIS 3.3 1.8 - - - -
38M ASN* 1.3 77.4 - - - +
40M PHE* 1.3 75.9 + + - +
43M GLY* 3.0 27.8 + - - -
95M MET* 3.7 10.7 - - + +
144T TRP* 3.9 24.5 - + - -
145T MET* 3.6 47.1 - - + -
148T ALA* 3.6 17.9 - - + +
149T PHE* 4.3 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M HIS 5.1 0.6 + - - -
38M ASN 3.4 0.6 - - - -
39M PHE* 1.3 87.7 - + - +
41M THR* 1.3 62.3 + - + +
43M GLY* 3.9 0.7 - - - -
44M GLU* 3.4 30.1 + - - +
41T THR* 3.7 15.5 - - - +
42T LEU* 4.0 20.9 - - + -
45T LYS* 3.8 34.1 - - + -
145T MET* 4.0 41.3 - - + -
146T PHE* 3.3 42.6 - + - -
149T PHE* 3.9 27.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M HIS 5.3 1.1 - - - +
38M ASN* 3.6 19.7 + - - +
40M PHE* 1.3 73.6 - - + +
42M LEU* 1.3 70.6 + - - +
44M GLU* 3.5 9.1 + - - +
45M LYS* 3.3 23.4 + - - +
149M PHE* 5.9 1.0 - - - -
38T ASN* 5.4 1.1 - - - +
41T THR* 3.8 26.0 - - + +
37X HIS 5.6 2.6 + - - +
40X PHE* 4.0 15.8 - - - +
41X THR* 3.5 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M MET* 3.8 11.9 - - + -
38M ASN* 3.0 18.9 + - + +
41M THR* 1.3 81.5 + - - +
43M GLY* 1.3 56.4 + - - +
45M LYS* 3.2 9.7 + - + +
46M MET* 3.0 31.5 + - + +
95M MET* 3.4 30.3 - - + -
99M MET* 4.0 25.1 - - + -
146M PHE* 4.6 0.7 - - + -
149M PHE* 3.4 44.6 - - + -
40X PHE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M HIS* 3.2 39.1 + - - -
34M MET* 3.7 6.0 - - - -
39M PHE* 3.0 21.1 + - - -
40M PHE 3.9 1.3 - - - -
41M THR 3.3 0.4 - - - -
42M LEU* 1.3 75.4 - - - +
44M GLU* 1.3 62.6 + - - +
46M MET 3.3 1.4 + - - -
47M ASP* 3.2 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M PHE* 3.4 19.4 + - - +
41M THR* 4.0 6.4 - - - +
42M LEU 3.4 0.2 - - - -
43M GLY* 1.3 74.5 - - - +
45M LYS* 1.3 66.9 + - + +
47M ASP* 3.4 13.3 + - - +
48M ASP* 3.1 29.9 + - - +
45T LYS* 4.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M THR 3.3 13.7 + - - +
42M LEU* 3.2 14.8 + - + +
44M GLU* 1.3 81.6 - - + +
46M MET* 1.3 66.3 + - + +
48M ASP* 3.4 18.0 + - - +
49M LEU* 3.0 41.5 + - - +
142M HIS* 4.6 8.7 + - - -
145M MET* 4.7 4.6 - - - +
146M PHE* 3.9 23.5 - - + -
40X PHE* 3.4 46.6 - - + -
44X GLU* 5.3 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ILE* 3.2 30.0 - - + +
30M ILE* 3.8 22.7 - - + -
31M HIS* 3.9 17.0 - - + +
34M MET* 3.5 18.8 - - + -
42M LEU* 3.0 21.9 + - + +
43M GLY 3.7 7.6 - - - +
44M GLU 3.2 0.2 - - - -
45M LYS* 1.3 78.8 - - + +
47M ASP* 1.3 55.8 + - - +
49M LEU* 3.2 12.1 + - + -
50M TYR* 2.8 33.2 + - - +
99M MET* 4.1 13.5 - - + -
102M LEU* 4.6 7.2 - - + -
146M PHE* 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS* 5.5 4.9 - - - -
31M HIS* 3.5 25.7 + - - -
43M GLY 3.2 14.5 + - - +
44M GLU* 3.5 16.6 - - - +
46M MET* 1.3 76.5 - - - +
48M ASP* 1.3 65.9 + - - +
50M TYR* 3.7 6.5 - - - +
51M SER* 3.2 25.8 + - - -
58O ASP* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU* 3.1 17.3 + - - +
45M LYS* 3.7 23.7 - - - +
47M ASP* 1.3 80.1 - - - +
49M LEU* 1.3 59.8 + - + +
51M SER* 3.6 5.0 + - - -
52M GLU* 2.9 30.8 + - - +
142M HIS* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M PHE* 4.7 3.6 - - + -
27M ILE* 4.0 12.6 - - + -
45M LYS* 3.0 25.3 + - - +
46M MET* 3.6 14.4 - - + +
48M ASP* 1.3 75.6 - - + +
50M TYR* 1.3 67.3 + - - +
52M GLU* 4.5 2.9 - - - +
53M PHE* 2.9 45.1 + - + +
102M LEU* 3.8 39.5 - - + -
106M LEU* 5.4 3.4 - - + -
142M HIS* 3.8 34.1 - - + +
146M PHE* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M THR* 3.4 53.7 + - + +
25M VAL* 6.0 1.0 - - + +
27M ILE* 4.0 15.3 - - + +
28M HIS* 3.2 44.0 + + + -
46M MET 2.8 21.7 + - - +
47M ASP* 3.7 7.4 - - - +
49M LEU* 1.3 72.5 - - - +
51M SER* 1.3 63.3 + - - +
54M GLY* 3.0 27.0 + - - -
21O ASN* 5.6 0.7 + - - -
24O THR* 5.9 2.4 - - - +
50O TYR* 4.7 12.8 + + - -
54O GLY* 5.9 3.5 - - - -
57O MET* 4.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M ASP 3.2 12.6 + - - -
48M ASP* 3.9 6.9 - - - -
50M TYR* 1.3 82.1 - - - +
52M GLU* 1.3 68.1 + - - +
54M GLY* 3.3 1.5 + - - -
55M GLU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ASP 2.9 20.1 + - - +
49M LEU* 3.9 3.9 - - - +
51M SER* 1.3 79.5 - - - +
53M PHE* 1.3 68.0 + - + +
55M GLU* 3.4 6.7 + - + +
56M GLN* 3.0 34.6 + - + +
138M SER* 2.4 30.9 + - - -
142M HIS* 2.6 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 4.1 17.3 - - + +
23M PHE* 3.7 37.0 - + + -
24M THR* 4.3 11.9 - - - +
27M ILE* 4.6 1.1 - - + -
49M LEU* 2.9 38.4 + - + +
52M GLU* 1.3 85.6 - - + +
54M GLY* 1.3 59.7 + - - +
56M GLN* 3.4 34.9 + - - +
57M MET* 3.0 27.4 + - - +
106M LEU* 3.9 13.2 - - + -
109M LEU* 4.6 6.1 - - + -
138M SER* 5.1 0.2 - - - -
139M ILE* 3.9 28.0 - - + -
142M HIS* 4.0 23.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M THR* 4.0 8.9 + - - -
50M TYR* 3.0 19.9 + - - -
51M SER* 3.3 2.0 + - - -
53M PHE* 1.3 77.6 - - - +
55M GLU* 1.3 54.8 + - - +
57M MET* 3.5 13.5 - - - +
58M ASP* 3.1 33.2 + - - +
50O TYR* 5.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M SER 3.0 16.8 + - - +
52M GLU* 3.6 7.0 - - + +
54M GLY* 1.3 73.5 - - - +
56M GLN* 1.3 65.4 + - - +
57M MET 3.2 1.3 - - - -
58M ASP* 3.3 15.6 + - - +
59M GLU* 2.7 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 4.3 6.4 - - + +
52M GLU* 3.0 32.7 + - + +
53M PHE* 3.4 40.0 + - + +
55M GLU* 1.3 73.7 - - - +
57M MET* 1.3 59.4 + - - +
59M GLU* 3.1 4.5 + - - +
60M VAL* 2.9 32.5 + - - +
113M TYR* 2.9 27.7 + - - -
135M PHE* 3.3 62.3 + - + +
138M SER* 4.8 1.6 - - - -
139M ILE* 4.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M VAL* 4.1 11.3 - - - +
20M LEU* 3.7 28.5 - - + -
21M ASN* 3.4 40.8 - - - +
53M PHE 3.0 13.9 + - - +
54M GLY* 3.5 10.8 - - - +
56M GLN* 1.3 80.3 - - - +
58M ASP* 1.3 72.6 + - - +
60M VAL* 3.8 2.8 - - - +
61M ALA* 3.0 23.7 + - - +
28O HIS* 3.8 22.0 - - + +
32O TRP* 3.7 19.5 - - + -
50O TYR* 4.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M GLY 3.1 16.9 + - - +
55M GLU* 3.8 20.8 - - - +
56M GLN 3.3 0.2 - - - -
57M MET* 1.3 84.1 - - - +
59M GLU* 1.3 59.4 + - - +
61M ALA* 3.4 4.3 + - - +
62M GLU* 2.9 48.0 + - - +
28O HIS* 3.1 38.7 + - - -
32O TRP* 4.0 6.1 - - - +
50O TYR* 5.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M GLU* 2.7 40.9 + - - +
56M GLN 3.5 7.6 - - - +
58M ASP* 1.3 74.1 - - - +
60M VAL* 1.3 59.8 + - - +
62M GLU* 4.2 6.4 - - - +
63M ARG* 2.9 31.7 + - - +
131M MET* 3.7 12.1 - - + +
135M PHE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 3.3 40.2 - - + +
16M GLN* 4.5 5.8 - - + -
17M VAL* 3.5 17.9 - - + +
20M LEU* 4.2 14.4 - - + -
56M GLN 2.9 18.4 + - - +
57M MET* 3.8 6.7 - - - +
59M GLU* 1.3 74.4 - - - +
61M ALA* 1.3 58.9 + - - +
63M ARG* 3.3 2.6 + - - +
64M LEU* 2.9 27.2 + - - +
113M TYR* 4.7 2.5 - - - +
131M MET* 4.1 14.6 - - + -
132M LEU* 5.2 3.6 - - + -
135M PHE* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M VAL* 4.1 16.4 - - + -
57M MET 3.0 18.6 + - - +
58M ASP 3.8 1.8 - - - +
60M VAL* 1.3 77.8 - - - +
62M GLU* 1.3 56.2 + - - +
64M LEU* 3.3 7.4 + - - +
65M LEU* 3.1 31.4 + - - +
71M PRO* 3.7 10.2 - - + +
32O TRP* 3.5 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M ASP* 2.9 36.0 + - - +
59M GLU* 4.2 6.4 - - - +
61M ALA* 1.3 70.3 - - - +
63M ARG* 1.3 60.0 + - - +
65M LEU* 3.5 10.3 + - + +
66M ALA* 3.1 26.7 + - - +
31O HIS* 4.1 15.7 + - - +
32O TRP* 4.7 11.8 + - + +
141Q LYS* 2.8 40.4 + - + +
144Q TRP* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 4.0 8.5 - - + -
59M GLU 2.9 20.9 + - - +
60M VAL 3.6 3.4 - - - +
62M GLU* 1.3 74.8 - - - +
64M LEU* 1.3 65.8 + - - +
66M ALA* 3.2 16.0 + - - +
67M ILE* 3.3 33.5 + - + +
125M ASP* 2.8 31.9 + - - -
127M VAL* 3.3 36.5 - - - +
128M THR* 2.9 21.3 + - - +
131M MET* 3.8 21.1 - - + -
136Q LYS* 4.3 4.9 - - - +
137Q ALA 5.2 0.6 + - - -
140Q ASP* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M LYS* 3.4 46.4 - - + +
13M LEU* 4.1 15.0 - - + +
14M ASN* 3.3 44.6 - - + +
17M VAL* 4.8 3.4 - - + -
60M VAL 2.9 15.0 + - - +
61M ALA 3.3 8.9 + - - +
63M ARG* 1.3 73.7 - - - +
65M LEU* 1.3 59.9 + - - +
67M ILE* 3.3 12.8 - - + +
69M GLY* 3.0 27.7 + - - -
70M SER 4.0 9.9 - - - +
71M PRO* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ALA 3.1 21.2 + - - +
62M GLU* 3.6 14.8 - - - +
64M LEU* 1.3 77.3 - - - +
66M ALA* 1.3 61.4 + - - +
68M GLY* 3.2 6.4 + - - -
69M GLY 3.9 11.3 + - - +
71M PRO* 3.5 31.2 - - + +
32O TRP* 3.6 42.0 - - + +
33O TYR* 5.1 5.8 - - + -
144Q TRP* 3.7 33.4 - - + +
154Q PRO* 3.1 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLU 3.1 17.8 + - - +
63M ARG* 3.2 21.9 + - - +
65M LEU* 1.3 76.8 - - - +
67M ILE* 1.3 60.1 + - - +
68M GLY 3.4 1.1 + - - -
140Q ASP* 3.9 31.9 - - + +
141Q LYS* 4.6 5.2 - - + +
144Q TRP* 4.0 15.0 - - + -
154Q PRO* 4.2 11.0 - - - +
155Q LEU* 4.3 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M THR* 4.2 15.5 - - + -
10M LYS* 3.7 36.2 - - + +
13M LEU* 3.9 27.1 - - + -
63M ARG* 3.3 42.1 + - - +
64M LEU* 3.3 14.4 - - - +
66M ALA* 1.3 74.0 - - - +
68M GLY* 1.3 57.1 + - - +
125M ASP* 4.1 7.0 - - - +
155Q LEU* 3.7 19.2 - - - +
----------------------------------------------------------
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