Contacts of the helix formed by residues 38 - 67 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 5.3 2.6 - - - +
37E HIS* 3.2 53.1 + - - +
38E ASN* 5.7 2.8 - - - +
36L GLY 3.0 2.2 + - - -
37L HIS* 1.3 88.8 + - - +
39L PHE* 1.3 63.6 + - - +
40L PHE 3.3 2.2 - - - -
41L THR* 3.5 12.4 + - - +
42L LEU* 3.0 42.8 + - + +
95L MET* 3.8 15.8 - - + +
149L PHE* 4.0 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 4.1 22.9 - + - -
145C MET* 3.9 46.7 - - + -
148C ALA* 3.8 14.1 - - + -
149C PHE* 4.1 14.7 - - + +
31L HIS* 4.4 14.1 - + - -
32L TRP 5.6 0.2 - - - -
34L MET* 3.3 40.8 - - + +
36L GLY 3.2 16.3 + - - +
37L HIS 3.4 2.0 + - - -
38L ASN* 1.3 78.0 - - - +
40L PHE* 1.3 80.0 + + - +
43L GLY* 2.9 28.0 + - - -
95L MET* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 3.7 15.5 - - + +
42C LEU* 3.9 15.7 - - + -
45C LYS* 3.8 41.1 - - + -
145C MET* 4.0 28.0 - - + -
146C PHE* 3.7 35.9 - + - -
149C PHE* 3.8 34.3 - + + -
37L HIS 5.1 0.6 + - - -
38L ASN 3.3 0.4 - - - -
39L PHE* 1.3 95.9 - + - +
41L THR* 1.3 62.9 + - - +
43L GLY* 3.2 0.7 + - - -
44L GLU* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 3.4 26.7 - - + +
37E HIS 4.9 5.9 + - - +
40E PHE* 4.5 13.3 - - - +
41E THR* 3.3 35.2 - - + +
37L HIS 5.6 0.2 - - - +
38L ASN* 3.5 14.8 + - + +
40L PHE* 1.3 76.9 - - - +
42L LEU* 1.3 68.4 + - - +
43L GLY 3.3 0.2 + - - -
44L GLU* 3.5 6.5 + - - +
45L LYS* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.1 30.1 - - + -
34L MET* 3.8 13.9 - - + -
38L ASN* 3.0 18.8 + - + +
41L THR* 1.3 78.6 + - - +
43L GLY* 1.3 59.8 + - - +
45L LYS* 3.8 4.3 - - + +
46L MET* 2.9 34.1 + - + +
95L MET* 3.5 25.6 - - + -
99L MET* 3.9 19.3 - - + -
146L PHE* 4.4 10.8 - - + -
149L PHE* 3.2 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L HIS* 3.5 37.8 + - - -
34L MET* 3.7 2.9 - - - -
39L PHE* 2.9 21.6 + - - -
40L PHE 3.2 1.5 + - - -
42L LEU* 1.3 74.3 - - - +
44L GLU* 1.3 64.4 + - - +
46L MET* 3.2 3.3 + - - -
47L ASP* 3.1 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 5.2 5.2 - - - +
40L PHE 3.1 14.6 + - - +
41L THR* 3.9 6.3 - - - +
43L GLY* 1.3 74.3 - - - +
45L LYS* 1.3 59.0 + - + +
47L ASP* 3.1 13.7 + - + +
48L ASP* 3.1 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 3.3 56.8 - - + -
44E GLU* 4.8 9.2 - - - +
41L THR* 3.0 21.5 + - - +
42L LEU* 3.8 8.3 - - + +
43L GLY 3.3 0.2 - - - -
44L GLU* 1.3 77.1 - - + +
46L MET* 1.3 72.9 + - + +
48L ASP* 3.5 22.5 + - - +
49L LEU* 3.1 26.1 + - - +
142L HIS* 5.0 6.1 + - - -
145L MET* 4.5 11.7 - - - +
146L PHE* 4.3 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L ILE* 3.2 30.9 - - + +
30L ILE* 4.0 22.2 - - + -
31L HIS* 3.9 18.2 - - + +
34L MET* 3.4 19.3 - - + -
42L LEU* 2.9 24.3 + - + +
43L GLY 3.2 4.4 + - - +
45L LYS* 1.3 77.4 - - + +
47L ASP* 1.3 60.2 + - - +
49L LEU* 3.3 25.2 + - + -
50L TYR* 3.0 25.5 + - - +
99L MET* 4.5 10.3 - - - -
102L LEU* 4.4 11.9 - - + -
146L PHE* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J ASP* 5.7 1.0 - - - +
28L HIS* 5.3 6.8 - - - -
31L HIS* 3.2 33.0 + - - -
43L GLY 3.1 11.0 + - - +
44L GLU* 3.1 13.4 + - + +
46L MET* 1.3 76.0 - - - +
48L ASP* 1.3 65.3 + - - +
50L TYR* 3.4 6.1 + - - +
51L SER* 3.2 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L GLU* 3.1 30.0 + - - +
45L LYS* 3.9 26.6 - - - +
47L ASP* 1.3 77.8 - - - +
49L LEU* 1.3 57.6 + - + +
51L SER* 3.5 5.2 + - - -
52L GLU* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L PHE* 5.3 1.8 - - + -
27L ILE* 4.3 12.1 - - + -
45L LYS* 3.1 13.4 + - - +
46L MET* 3.7 23.1 - - + +
47L ASP 3.3 0.2 - - - -
48L ASP* 1.3 73.6 - - + +
50L TYR* 1.3 56.3 + - - +
52L GLU* 3.7 3.1 - - - +
53L PHE* 2.8 61.7 + - + +
102L LEU* 4.1 14.8 - - + -
106L LEU* 5.5 2.0 - - + -
142L HIS* 3.4 42.6 - - + +
146L PHE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN* 5.2 2.3 + - - -
24J THR* 5.9 2.8 - - - +
50J TYR* 4.9 10.2 + + - -
54J GLY* 6.5 0.9 - - - -
57J MET* 4.5 7.6 - - - +
58J ASP* 5.4 2.2 - - - -
24L THR* 3.3 54.7 + - + +
25L VAL* 5.2 1.3 - - - +
27L ILE* 4.0 13.6 - - + +
28L HIS* 3.2 47.2 + + + +
46L MET 3.0 17.2 + - - +
47L ASP* 3.5 9.0 - - - +
48L ASP 3.3 0.2 - - - -
49L LEU* 1.3 72.7 - - - +
51L SER* 1.3 72.3 + - - +
53L PHE* 3.9 0.4 - - - -
54L GLY* 3.0 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ASP 3.2 9.9 + - - -
48L ASP* 3.9 9.0 - - - -
50L TYR* 1.3 86.5 - - - +
52L GLU* 1.3 63.7 + - - +
54L GLY* 3.2 1.4 + - - -
55L GLU* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ASP 3.0 19.1 + - - +
49L LEU* 3.8 7.0 - - - +
51L SER* 1.3 77.3 - - - +
53L PHE* 1.3 66.1 + - + +
55L GLU* 3.2 18.5 + - - +
56L GLN* 3.1 33.3 + - + +
138L SER* 2.4 32.0 + - - -
142L HIS* 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 4.1 17.7 - - + +
23L PHE* 3.8 34.1 - + + -
24L THR* 4.2 11.0 + - - +
27L ILE* 4.7 3.4 - - + -
49L LEU* 2.8 57.6 + - + +
50L TYR 4.5 1.1 - - - +
52L GLU* 1.3 77.8 - - + +
54L GLY* 1.3 62.9 + - - +
55L GLU 3.2 0.2 - - - -
56L GLN* 3.5 36.7 - - - +
57L MET* 3.1 22.5 + - - +
106L LEU* 3.8 20.9 - - + -
109L LEU* 4.4 7.9 - - + -
139L ILE* 3.9 18.8 - - + -
142L HIS* 4.2 11.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J TYR* 6.0 2.0 - - - -
24L THR* 4.0 10.0 + - - -
50L TYR* 3.0 15.9 + - - -
51L SER 3.8 2.9 - - - -
53L PHE* 1.3 75.3 - - - +
55L GLU* 1.3 59.5 + - - +
57L MET* 3.4 12.1 + - - +
58L ASP* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L SER* 3.0 22.6 + - - +
52L GLU* 3.3 20.6 - - + +
54L GLY* 1.3 75.9 - - - +
56L GLN* 1.3 61.6 + - - +
58L ASP* 3.3 9.7 + - - +
59L GLU* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 4.3 5.5 - - + +
52L GLU* 3.1 27.9 + - + +
53L PHE* 3.5 42.3 - - + +
54L GLY 3.4 0.2 - - - -
55L GLU* 1.3 74.9 - - - +
57L MET* 1.3 53.5 + - - +
59L GLU* 3.1 4.9 + - - +
60L VAL* 2.7 38.2 + - - +
113L TYR* 2.9 27.2 + - - -
135L PHE* 3.5 60.2 + - + +
138L SER* 4.6 1.4 + - - -
139L ILE* 4.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J HIS* 3.6 35.2 - - + +
32J TRP* 3.8 18.4 - - + -
50J TYR* 4.7 5.2 - - - +
17L VAL* 4.1 11.1 - - - +
20L LEU* 3.8 30.1 - - + +
21L ASN* 3.3 40.8 - - - +
24L THR* 5.8 2.7 - - + +
53L PHE 3.1 14.6 + - - +
54L GLY* 3.5 11.0 - - - +
56L GLN* 1.3 78.4 - - - +
58L ASP* 1.3 69.6 + - - +
60L VAL* 3.1 4.6 + - - +
61L ALA* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J HIS* 2.8 40.5 + - - -
32J TRP* 4.4 4.9 - - - +
47J ASP* 5.2 4.9 - - - +
50J TYR* 5.5 0.4 - - - -
54L GLY 3.0 15.4 + - - +
55L GLU* 3.4 11.9 - - - +
57L MET* 1.3 82.8 - - - +
59L GLU* 1.3 58.0 + - + +
61L ALA* 3.4 4.5 + - - +
62L GLU* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 4.7 13.4 + - - +
55L GLU* 3.0 25.5 + - - +
56L GLN 3.6 7.2 - - - +
58L ASP* 1.3 76.4 - - + +
60L VAL* 1.3 57.9 + - - +
62L GLU* 3.7 6.3 - - - +
63L ARG* 2.8 31.9 + - - +
131L MET* 3.8 11.7 - - - +
135L PHE* 3.9 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L LEU* 3.4 39.7 - - + +
16L GLN* 4.4 5.6 - - + -
17L VAL* 3.7 16.6 - - + +
20L LEU* 4.2 15.7 - - + -
56L GLN 2.7 20.7 + - - +
57L MET* 3.1 9.8 + - - +
59L GLU* 1.3 72.0 - - - +
61L ALA* 1.3 58.3 + - - +
63L ARG* 3.2 4.0 + - - +
64L LEU* 2.9 26.7 + - - +
113L TYR* 4.7 4.0 - - - +
131L MET* 4.1 13.2 - - + -
132L LEU* 5.2 4.7 - - + -
135L PHE* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J TRP* 3.6 41.1 - - + -
17L VAL* 4.3 11.4 - - + -
57L MET 3.0 12.9 + - - +
58L ASP 3.9 1.8 - - - +
60L VAL* 1.3 75.9 - - - +
62L GLU* 1.3 58.2 + - - +
64L LEU* 3.3 6.7 + - - +
65L LEU* 2.8 33.0 + - - +
71L PRO* 4.1 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 2.8 43.1 + - - +
144B TRP* 3.9 30.2 - - + -
31J HIS* 4.1 20.4 + - - -
32J TRP* 4.7 12.0 + - + +
58L ASP* 2.9 33.0 + - - +
59L GLU* 3.9 2.6 - - - +
61L ALA* 1.3 75.9 - - - +
63L ARG* 1.3 61.2 + - - +
65L LEU* 3.4 8.7 + - - +
66L ALA* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 4.4 4.2 - - - +
137B ALA* 5.0 2.0 + - - +
140B ASP* 3.1 42.0 + - - +
141B LYS* 5.2 0.8 - - - +
13L LEU* 4.2 5.4 - - + -
59L GLU 2.8 17.8 + - - +
60L VAL 3.6 3.8 - - - +
62L GLU* 1.3 77.8 - - - +
64L LEU* 1.3 62.0 + - - +
66L ALA* 3.2 16.4 + - - +
67L ILE* 3.3 36.1 + - - +
125L ASP* 3.0 25.3 + - - -
127L VAL* 3.3 33.3 - - - +
128L THR* 3.1 22.3 + - - +
131L MET* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L LYS* 3.5 43.5 - - + +
13L LEU* 4.0 17.7 - - + +
14L ASN* 3.4 25.6 - - + +
17L VAL* 4.9 2.2 - - + -
60L VAL* 2.9 14.4 + - + +
61L ALA* 3.3 8.0 + - - +
63L ARG* 1.3 76.6 - - - +
65L LEU* 1.3 61.7 + - - +
66L ALA 3.3 0.3 + - - -
67L ILE* 3.4 6.9 + - + +
68L GLY 3.4 4.3 + - - -
69L GLY* 2.9 29.1 + - - -
70L SER 3.8 8.5 - - - +
71L PRO* 3.4 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 4.0 33.3 - - + +
154B PRO* 3.4 16.5 - - - +
32J TRP* 3.8 50.0 - - + +
33J TYR* 5.0 6.1 - - + -
61L ALA 2.8 25.9 + - - +
62L GLU* 3.6 9.2 - - - +
63L ARG 3.3 0.2 - - - -
64L LEU* 1.3 74.5 - - - +
66L ALA* 1.3 57.1 + - - +
68L GLY* 3.2 15.2 + - - -
69L GLY 3.6 12.4 + - - +
70L SER* 4.8 0.2 - - - -
71L PRO* 3.3 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP* 3.6 35.5 - - - +
141B LYS* 4.5 4.7 - - + +
143B ILE* 5.9 1.0 - - - +
144B TRP* 4.1 15.5 - - + -
154B PRO* 4.1 12.0 - - - +
155B LEU* 4.5 8.1 - - - +
62L GLU 3.2 14.9 + - - +
63L ARG* 3.2 17.6 + - - +
65L LEU* 1.3 77.9 - - - +
67L ILE* 1.3 58.1 + - - +
68L GLY 3.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.9 18.9 - - - +
9L THR* 3.8 29.6 - - + -
10L LYS* 3.7 37.7 + - + +
13L LEU* 4.0 13.9 - - + -
63L ARG* 3.3 47.1 + - - +
64L LEU* 3.5 13.5 - - + +
66L ALA* 1.3 76.5 - - - +
68L GLY* 1.3 56.5 + - - +
125L ASP* 4.3 6.3 - - - +
----------------------------------------------------------
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