Contacts of the helix formed by residues 58 - 87 (chain E) in PDB entry 1L8I
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 58 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 5.8 1.1 - - + -
58B ASN* 3.3 40.6 + - + +
60B ILE* 4.8 0.8 - - - +
56E GLY 3.5 0.2 + - - -
57E ALA* 1.3 75.5 - - + +
59E PHE* 1.3 64.7 + - - +
60E ILE 3.7 1.1 - - - -
61E ALA* 3.3 23.8 - - - +
62E VAL* 2.9 30.8 + - + +
114E VAL* 4.9 1.8 - - + -
115E GLN* 6.2 1.3 - - - +
118E LEU* 6.4 0.2 - - + -
165E ASN* 3.0 32.2 + - - +
58L ASN* 3.5 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E HIS 4.4 0.7 - - - -
54E MET* 3.4 41.2 - - + +
55E ARG* 4.4 0.2 - - - -
56E GLY 3.1 18.1 + - - +
57E ALA 3.1 2.8 - - - -
58E ASN* 1.3 78.9 - - - +
60E ILE* 1.3 83.0 + - - +
62E VAL* 3.6 1.7 - - - +
63E HIS* 2.7 59.0 + + + +
114E VAL* 3.9 9.6 - - + -
160L TRP* 4.3 8.3 - + - -
161L PHE* 3.7 32.5 - + - -
164L SER* 3.2 35.0 - - - +
165L ASN* 3.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B TRS 5.5 2.2 - - - +
59E PHE* 1.3 84.5 - - + +
61E ALA* 1.3 73.8 + - + +
63E HIS* 3.2 5.3 - - - +
64E GLU* 2.8 50.9 + - + +
58L ASN* 4.4 4.0 - - - +
61L ALA* 3.9 29.4 - - + +
62L VAL* 4.7 1.3 - - + +
65L MET* 3.9 19.3 - - + -
161L PHE* 3.6 44.0 - - + -
165L ASN* 3.2 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.0 18.6 - - + +
61B ALA* 4.0 16.6 - - + -
308B TRS 5.2 10.4 - - - +
58E ASN* 3.3 24.2 + - - +
59E PHE 3.4 0.6 - - - -
60E ILE* 1.3 83.0 - - + +
62E VAL* 1.3 58.2 + - - +
64E GLU* 3.6 7.5 + - - +
65E MET* 2.9 27.5 + - - +
61L ALA* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.9 1.1 - - + -
54E MET* 3.9 13.2 - - - -
58E ASN* 2.9 43.0 + - + +
59E PHE 3.0 3.4 + - - +
61E ALA* 1.3 72.5 - - - +
63E HIS* 1.3 63.6 + - - +
65E MET* 2.9 14.4 + - + +
66E LEU* 2.7 52.8 + - + +
114E VAL* 4.4 9.9 - - + -
118E LEU* 3.6 23.6 - - + -
165E ASN* 4.3 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E HIS* 2.8 81.8 + + - -
52E TRP* 4.8 0.6 - - - -
54E MET* 4.1 8.7 - - - -
59E PHE* 2.7 47.1 + + + +
60E ILE* 3.2 4.8 - - - +
62E VAL* 1.3 73.8 - - - +
64E GLU* 1.3 71.5 + - + +
66E LEU* 3.5 7.6 + - - +
67E ASP* 3.6 1.6 + - - -
82F GLU* 4.7 5.6 + - - -
160L TRP* 3.9 17.8 - + - -
161L PHE* 3.8 30.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B TRS 3.4 40.4 + - - +
60E ILE* 2.8 44.6 + - + +
61E ALA* 4.0 3.1 - - - +
63E HIS* 1.3 81.4 - - + +
65E MET* 1.3 66.9 + - - +
67E ASP* 3.0 25.1 + - - +
68E GLY* 3.3 3.8 + - - -
161L PHE* 4.9 4.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.1 19.1 - - + -
308B TRS 5.8 0.6 + - - -
61E ALA 2.9 15.8 + - - +
62E VAL* 2.9 32.8 + - + +
64E GLU* 1.3 76.5 - - - +
66E LEU* 1.3 67.3 + - + +
68E GLY* 3.0 12.8 + - - +
69E PHE* 3.3 47.8 + - + -
118E LEU* 5.0 2.2 - - + -
161E PHE* 3.9 23.6 - - + +
162E ILE* 4.5 8.3 - - + -
165E ASN* 3.7 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E THR* 3.5 29.8 - - + +
51E HIS* 4.2 11.0 - - + -
54E MET* 3.8 16.2 - - + -
62E VAL* 2.7 55.4 + - + +
63E HIS* 3.7 8.3 - - - +
64E GLU 3.2 0.2 - - - -
65E MET* 1.3 80.0 - - + +
67E ASP* 1.3 64.7 + - - +
69E PHE* 3.1 38.7 + - + +
70E ARG 3.1 9.7 + - - -
118E LEU* 5.8 0.7 - - + -
121E LEU* 4.0 24.7 - - + -
125E TYR* 5.0 1.1 - - - +
162E ILE* 5.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LYS* 3.2 26.6 + - - -
51E HIS* 3.3 24.0 + - - -
63E HIS* 3.6 3.7 + - - +
64E GLU* 3.0 15.6 + - - +
66E LEU* 1.3 77.5 - - - +
68E GLY* 1.3 65.8 + - - +
70E ARG* 2.9 39.1 + - - +
71E THR* 3.1 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU 3.3 4.3 + - - -
65E MET* 3.0 9.6 + - - -
67E ASP* 1.3 80.9 - - - +
69E PHE* 1.3 65.1 + - - +
71E THR* 3.2 14.7 + - - -
72E ALA* 3.3 11.1 + - - +
158E PHE* 5.1 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E MET* 3.3 45.5 + - + -
66E LEU* 3.1 24.8 + - + +
68E GLY* 1.3 76.2 - - - +
70E ARG* 1.3 64.4 + - - +
72E ALA* 3.0 4.3 + - - +
73E LEU* 2.8 26.8 + - - +
125E TYR* 3.6 24.9 - + - +
158E PHE* 3.4 49.4 - + + -
161E PHE* 3.8 24.2 - + + -
162E ILE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E SER* 4.4 18.8 - - - +
47E THR* 4.6 8.7 - - + +
48E LYS* 3.4 34.5 - - + +
66E LEU 3.1 7.3 + - - +
67E ASP* 2.9 36.5 + - - +
69E PHE* 1.3 78.1 - - - +
71E THR* 1.3 81.3 + - - +
73E LEU* 3.2 11.2 + - - +
74E ILE* 3.0 55.5 + - + +
70F ARG* 5.8 0.2 - - - +
74F ILE* 3.9 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E ASP 3.1 11.7 + - - -
68E GLY* 3.5 10.9 - - - -
70E ARG* 1.3 91.8 + - - +
72E ALA* 1.3 63.8 + - - +
74E ILE* 3.3 8.9 + - - +
75E CYS* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLY 3.3 5.9 + - - +
69E PHE 3.0 3.8 + - - +
71E THR* 1.3 77.7 - - - +
73E LEU* 1.3 67.3 + - - +
75E CYS* 3.1 8.2 + - - +
76E HIS* 3.0 31.5 + - + +
154E ASP* 4.1 13.7 - - - +
158E PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.0 17.8 - - + +
43E LEU* 4.2 14.6 - - + -
44E SER* 3.9 34.5 - - - +
47E THR* 4.0 2.0 - - - +
69E PHE 2.8 20.6 + - - +
70E ARG* 3.4 6.3 - - - +
72E ALA* 1.3 73.9 - - - +
74E ILE* 1.3 57.4 + - - +
76E HIS* 3.3 3.6 + - + +
77E LEU* 2.8 32.4 + - - +
125E TYR* 3.5 23.3 - - - +
155E LEU* 4.2 22.7 - - + -
158E PHE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E SER* 4.7 10.5 - - - +
70E ARG* 3.0 53.7 + - + +
71E THR* 3.7 5.6 - - - +
73E LEU* 1.3 76.6 - - - +
75E CYS* 1.3 57.8 + - - +
77E LEU* 3.4 17.2 - - + +
78E ALA* 2.9 33.6 + - + +
48F LYS* 5.3 3.8 - - + -
70F ARG* 4.1 34.5 - - - +
74F ILE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E THR* 3.1 14.0 + - + +
72E ALA* 3.1 13.5 + - - +
74E ILE* 1.3 74.4 - - - +
76E HIS* 1.3 68.4 + - - +
78E ALA* 3.9 3.6 - - - +
79E THR* 2.6 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.1 11.7 - + + -
72E ALA* 3.0 29.5 + - + +
73E LEU* 3.7 7.6 - - + +
75E CYS* 1.3 77.8 - - + +
77E LEU* 1.3 68.8 + - - +
79E THR* 2.9 18.7 + - - -
80E MET* 2.9 20.0 + - + +
147E ILE* 4.7 4.4 + - + +
150E ALA* 3.4 31.1 - - + +
151E ALA* 3.4 29.8 + - + +
154E ASP* 2.7 36.5 + - + +
155E LEU* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E VAL* 4.0 9.5 - - + +
40E PHE* 4.1 8.9 - - + +
41E ILE* 3.3 49.6 - - + +
44E SER* 4.7 5.6 - - - +
73E LEU 2.8 17.4 + - - +
74E ILE* 3.4 24.0 - - + +
76E HIS* 1.3 79.5 - - - +
78E ALA* 1.3 64.8 + - + +
80E MET* 3.0 18.3 + - - +
81E ALA* 3.0 19.1 + - - +
48F LYS* 5.9 1.1 - - + -
52F TRP* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 2.9 22.3 + - + +
75E CYS* 3.9 3.8 - - - +
77E LEU* 1.3 80.4 - - + +
79E THR* 1.3 57.7 + - - +
81E ALA* 3.2 1.6 + - - +
82E GLU* 2.8 40.4 + - - +
48F LYS* 3.7 27.8 - - - +
52F TRP* 3.9 12.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E CYS* 2.6 26.8 + - - -
76E HIS* 2.9 13.4 + - - -
78E ALA* 1.3 75.5 - - - +
80E MET* 1.3 62.8 + - - +
82E GLU* 3.3 11.8 + - - +
83E ARG* 3.1 20.6 + - - +
147E ILE* 4.0 17.0 - - + +
207E K 4.4 9.2 - - - -
208E K 4.0 10.2 - - - -
153I ARG* 3.6 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU* 3.6 20.7 - - + +
36E GLN* 3.7 25.8 - - + -
37E VAL* 4.0 9.4 - - + +
40E PHE* 3.6 39.9 - - + -
76E HIS* 2.9 13.9 + - + +
77E LEU* 3.3 34.3 - - - +
79E THR* 1.3 73.8 - - - +
81E ALA* 1.3 67.0 + - - +
83E ARG* 2.8 15.7 + - - +
84E ALA* 3.0 10.7 + - - +
147E ILE* 3.6 22.9 - - + -
148E LEU* 4.0 17.9 - - - -
151E ALA* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ASN* 6.0 0.2 - - - -
37E VAL* 3.8 14.5 - - + +
77E LEU 3.0 9.8 + - - +
78E ALA 3.2 2.7 + - - +
80E MET* 1.3 75.3 - - - +
82E GLU* 1.3 63.8 + - - +
84E ALA* 3.3 6.3 + - - +
85E VAL* 3.1 27.0 + - - +
91E ALA* 3.7 13.8 - - + +
52F TRP* 3.3 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ALA* 2.8 24.7 + - - +
79E THR* 3.5 5.5 - - - +
81E ALA* 1.3 76.1 - - - +
83E ARG* 1.3 57.3 + - - +
85E VAL* 3.3 7.4 + - - +
86E GLN* 2.8 41.8 + - - +
207E K 3.1 18.5 - - - -
208E K 3.9 20.2 - - - -
48F LYS* 5.0 1.0 + - - -
51F HIS* 4.4 13.5 + - - -
52F TRP* 4.0 14.2 + - + -
63F HIS* 4.7 4.7 - - - -
157I LYS* 4.1 11.1 + - - -
160I TRP* 3.9 29.4 - - + -
161I PHE* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASN* 4.8 0.4 - - - +
21E VAL* 5.5 0.2 - - - +
33E LEU* 3.6 16.8 - - + -
79E THR 3.1 6.5 + - - +
80E MET* 2.8 9.9 + - - +
82E GLU* 1.3 72.7 - - - +
84E ALA* 1.3 66.9 + - - +
86E GLN* 3.1 21.4 + - - +
87E LEU* 3.1 41.1 + - + +
141E ASP* 2.6 34.3 + - - -
143E ASP* 3.0 32.8 + - - +
144E THR* 3.6 7.2 + - - +
147E ILE* 3.6 32.3 - - + -
133I ARG* 4.1 4.9 - - - +
153I ARG* 5.1 4.8 + - - +
156I ASP* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL* 3.6 25.5 - - + +
33E LEU* 3.4 26.1 - - + +
34E ASN* 4.7 7.6 - - - +
37E VAL* 6.3 0.2 - - + -
80E MET 3.0 8.2 + - - +
81E ALA* 3.5 11.0 - - - +
82E GLU 3.3 0.2 - - - -
83E ARG* 1.3 78.0 - - - +
85E VAL* 1.3 61.8 + - + +
87E LEU* 3.1 11.9 + - - +
88E GLY 3.5 0.2 + - - -
89E GLY* 2.9 24.3 + - - -
91E ALA* 5.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ALA 3.1 14.8 + - - +
82E GLU* 3.6 9.2 - - - +
84E ALA* 1.3 73.3 - - - +
86E GLN* 1.3 67.3 + - - +
88E GLY* 3.1 12.6 + - - -
89E GLY 3.7 11.4 - - - +
91E ALA* 3.8 16.8 - - + +
52F TRP* 3.6 23.6 - - + +
53F ASN* 3.6 25.6 - - - +
54F MET 6.0 0.4 - - - +
55F ARG* 3.8 19.2 + - - +
160I TRP* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E THR* 4.0 19.4 + - - +
19E ASN* 4.3 9.0 + - - +
82E GLU* 2.8 28.4 + - - +
83E ARG* 3.1 45.5 + - - +
85E VAL* 1.3 76.4 - - - +
87E LEU* 1.3 60.0 + - + +
88E GLY 3.1 3.9 + - - -
207E K 3.3 21.8 - - - -
55F ARG* 5.5 0.7 + - - -
153I ARG* 4.7 4.1 + - - +
156I ASP* 3.9 15.3 - - + +
157I LYS* 3.7 18.4 - - - +
160I TRP* 3.7 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LEU* 4.2 2.8 - - - +
17E THR* 4.7 2.9 - - - -
19E ASN* 4.0 26.7 - - - +
21E VAL* 4.1 20.9 - - + -
25E GLU* 6.6 0.2 - - + -
26E LYS* 3.1 40.8 - - + +
29E THR* 3.5 37.5 - - + -
30E VAL* 4.0 10.4 - - + +
83E ARG* 3.1 31.4 + - + +
84E ALA* 3.1 9.4 + - - +
86E GLN* 1.3 76.5 - - - +
88E GLY* 1.3 58.7 + - - +
89E GLY 3.4 1.5 + - - -
141E ASP* 4.1 11.4 - - + +
----------------------------------------------------------
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