Contacts of the helix formed by residues 45 - 74 (chain E) in PDB entry 2XQL
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 ALA 45 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ARG* 5.3 2.5 + - - +
27E VAL* 5.6 0.3 - - - +
31E HIS* 4.9 4.8 - - - -
44E GLY* 1.3 71.7 - - - -
46E GLY* 1.3 63.3 + - - +
48E PRO* 3.5 15.4 - - - +
49E VAL* 4.1 5.5 - - - +
121F TYR* 4.2 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLY 3.6 0.2 - - - -
45E ALA* 1.3 77.1 - - - +
47E ALA* 1.3 66.8 + - - +
49E VAL* 2.9 15.7 - - - +
50E TYR* 2.8 26.2 + - - +
91F SER* 3.8 13.2 - - - -
118F VAL* 3.8 11.0 - - - +
121F TYR* 5.2 2.7 - - - -
122F THR* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 5.3 4.7 - - + -
43E VAL* 4.7 5.2 - - + -
44E GLY 3.9 9.5 + - - +
46E GLY* 1.3 79.1 - - - +
48E PRO* 1.3 72.1 - - + +
50E TYR* 3.5 1.9 - - - +
51E LEU* 3.0 21.7 + - - +
89F ILE* 3.6 27.6 - - + +
90F THR 4.3 2.7 - - - -
91F SER* 4.0 8.0 - - - +
94F ILE* 4.0 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ARG* 4.8 0.9 - - - +
27E VAL* 3.7 16.4 - - + +
30E VAL* 3.7 13.6 - - + +
31E HIS* 3.2 53.6 - - + +
34E LEU* 4.9 4.5 - - + -
43E VAL* 4.6 3.1 - - + -
44E GLY 3.5 9.4 - - - +
45E ALA 3.5 12.3 - - - +
47E ALA* 1.3 95.3 - - + +
49E VAL* 1.3 53.4 + - - +
51E LEU* 4.4 1.1 - - + -
52E ALA* 2.7 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA* 3.3 34.3 - - + -
23E LEU* 3.7 7.3 - - + +
27E VAL* 4.0 17.3 - - + -
45E ALA 4.1 4.0 - - - +
46E GLY* 2.9 37.2 - - - +
48E PRO* 1.3 80.8 - - - +
50E TYR* 1.3 61.7 + - - +
52E ALA* 4.4 1.8 - - - -
53E ALA* 3.0 24.3 + - - +
117F ALA* 4.2 6.9 - - - +
118F VAL* 3.8 16.6 - - + -
121F TYR* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLY 2.8 17.1 + - - +
47E ALA 3.5 3.6 - - - +
49E VAL* 1.3 76.4 - - - +
51E LEU* 1.3 62.9 + - - +
53E ALA* 2.9 17.2 + - - +
54E VAL* 2.9 33.8 + - + +
91F SER* 4.1 18.8 - - - -
94F ILE* 3.6 19.7 - - + -
95F GLN* 2.6 61.3 + - + +
98F VAL* 4.6 2.9 - - + -
110F ALA 4.1 2.5 - - - -
111F VAL* 3.2 22.3 + - - +
114F GLY* 3.8 16.2 - - - -
115F THR* 3.9 4.3 - - - -
118F VAL* 3.4 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL* 4.0 4.5 - - + -
34E LEU* 3.6 33.4 - - + -
47E ALA 3.0 14.8 + - - +
48E PRO* 3.9 3.1 - - + +
50E TYR* 1.3 73.2 - - - +
52E ALA* 1.3 65.9 + - - +
54E VAL* 3.2 3.7 + - + +
55E LEU* 2.9 50.2 + - + +
70F PHE* 3.8 21.5 - - + +
73F ILE* 4.3 21.8 - - + -
74F ALA* 4.7 8.7 - - + -
94F ILE* 3.9 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 4.3 11.7 - - + -
25E PHE* 3.8 15.9 - - + +
27E VAL* 4.2 16.4 - - + -
30E VAL* 4.1 21.5 - - + +
48E PRO 2.7 23.8 + - - +
49E VAL* 3.9 4.0 - - - +
51E LEU* 1.3 72.8 - - - +
53E ALA* 1.3 57.8 + - - +
55E LEU* 3.3 5.8 + - - +
56E GLU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 3.9 15.9 - - + +
49E VAL 3.0 15.8 + - - +
50E TYR 2.9 13.4 + - - +
52E ALA* 1.3 77.5 - - - +
54E VAL* 1.3 55.2 + - - +
56E GLU* 3.4 3.1 + - - +
57E TYR* 3.0 27.6 + - - +
113F GLU* 4.0 11.0 - - + +
114F GLY* 3.8 11.9 - - - -
117F ALA* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 2.9 32.8 + - + +
51E LEU* 3.2 7.8 + - - +
53E ALA* 1.3 73.2 - - - +
55E LEU* 1.3 66.5 + - - +
57E TYR* 3.3 5.5 + - - +
58E LEU* 3.0 39.9 + - + +
69F ILE* 4.7 0.2 - - + -
73F ILE* 4.2 12.1 - - + -
94F ILE* 5.2 0.2 - - + -
98F VAL* 3.9 20.4 - - + -
102F LEU* 4.4 1.1 - - + -
110F ALA* 3.6 41.1 - - + +
113F GLU* 5.6 0.4 - - - -
114F GLY* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.9 14.1 - - + -
30E VAL* 4.3 14.8 - - + -
51E LEU* 2.9 44.4 + - + +
52E ALA* 3.5 4.5 - - - +
54E VAL* 1.3 78.5 - - - +
56E GLU* 1.3 56.5 + - - +
58E LEU* 3.5 4.8 + - - +
59E THR* 2.8 34.4 + - - -
37F TYR* 5.0 1.6 - - - +
65F PHE* 4.9 1.7 - - - -
66F VAL* 4.2 22.2 - - + +
69F ILE* 3.3 34.8 - - + -
70F PHE* 4.0 25.1 - - + -
73F ILE* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLY 5.2 0.5 - - - +
23E LEU* 3.2 20.8 - - + +
24E GLN* 2.6 52.3 + - - +
25E PHE* 3.3 27.7 + - + +
52E ALA 3.0 15.2 + - - +
53E ALA* 3.7 5.2 - - - +
55E LEU* 1.3 76.0 - - - +
57E TYR* 1.3 64.3 + - - +
59E THR* 3.3 2.4 + - - -
60E ALA* 2.9 23.6 + - + +
44F VAL* 4.1 11.6 - - + +
47F GLN* 3.9 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ALA 3.0 15.1 + - - +
54E VAL* 3.4 8.5 - - - +
56E GLU* 1.3 75.8 - - - +
58E LEU* 1.3 82.7 + - + +
60E ALA* 2.9 11.7 + - + +
61E GLU* 2.9 58.1 + - + +
106F LEU* 3.6 31.5 + - + +
109F HIS* 3.1 33.5 + + + +
110F ALA* 3.7 24.9 - - + -
113F GLU* 4.1 28.0 - - + -
103G ALA* 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 3.0 20.2 + - + +
55E LEU* 3.9 2.0 - - - +
57E TYR* 1.3 88.6 - - + +
59E THR* 1.3 63.1 + - - +
61E GLU* 3.2 4.6 + - + +
62E ILE* 3.0 29.6 + - - +
93E LEU* 4.9 5.2 - - + -
96E LEU* 4.5 10.5 - - + -
65F PHE* 3.7 21.5 - - + -
69F ILE* 3.4 34.3 - - + -
102F LEU* 3.9 33.9 - - + -
106F LEU* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.1 32.9 - - + -
55E LEU 2.8 24.0 + - - -
56E GLU 3.4 4.9 - - - -
57E TYR 3.1 0.2 - - - -
58E LEU* 1.3 76.2 - - - +
60E ALA* 1.3 59.8 + - - +
62E ILE* 3.7 2.6 - - - +
63E LEU* 2.9 48.6 + - + +
41F VAL* 4.2 8.3 - - + -
44F VAL* 4.3 5.2 - - + -
62F MET* 3.7 24.0 - - + -
65F PHE* 4.2 4.6 - - - -
66F VAL* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU* 2.9 14.3 + - + +
57E TYR* 3.3 12.3 - - + +
59E THR* 1.3 76.1 - - - +
61E GLU* 1.3 54.4 + - - +
63E LEU* 3.3 4.1 + - - +
64E GLU* 2.8 37.6 + - - +
44F VAL* 3.7 22.0 - - + +
47F GLN* 5.5 6.7 - - - +
48F VAL* 4.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 2.9 55.5 + - + +
58E LEU* 3.2 11.9 + - + +
60E ALA* 1.3 74.7 - - - +
62E ILE* 1.3 67.3 + - + +
64E GLU* 3.0 14.7 + - - +
65E LEU* 2.9 40.8 + - + +
90E ASP* 5.3 2.1 - - - +
93E LEU* 5.1 3.9 - - + +
106F LEU* 4.5 15.9 - - + +
109F HIS* 5.2 0.3 - - - -
101G THR* 6.1 0.2 - - - -
102G ILE 5.2 0.3 - - - +
103G ALA* 3.9 22.1 - - - +
104G GLN* 3.8 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU* 3.0 11.5 + - - +
59E THR 3.7 7.4 - - - +
61E GLU* 1.3 74.2 - - + +
63E LEU* 1.3 60.3 + - - +
65E LEU* 3.6 3.7 + - - +
66E ALA* 2.9 31.2 + - - +
83E LEU* 4.6 7.1 - - + +
86E ALA* 4.5 3.0 - - + +
87E ILE* 4.9 15.7 - - + -
93E LEU* 3.6 40.6 - - + -
97E LEU* 5.1 2.9 - - + -
62F MET* 3.4 37.7 - - + -
65F PHE* 3.9 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR* 2.9 28.2 + - + +
60E ALA* 3.6 5.2 - - - +
62E ILE* 1.3 78.5 - - - +
64E GLU* 1.3 57.5 + - - +
66E ALA* 3.6 3.4 - - - +
67E GLY* 2.9 23.9 + - - -
78E ILE* 4.0 8.3 - - + +
83E LEU* 4.8 3.8 - - + -
41F VAL* 3.5 34.3 - - + +
44F VAL* 4.4 3.1 - - + -
45F LEU* 3.8 28.8 - - + +
48F VAL* 4.5 8.6 - - + +
54F ILE* 3.9 27.4 - - + -
62F MET* 4.1 22.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
60E ALA 2.8 18.4 + - - +
61E GLU* 3.0 9.3 + - - +
63E LEU* 1.3 74.2 - - - +
65E LEU* 1.3 68.8 + - + +
67E GLY* 2.9 12.6 + - - -
68E ASN* 2.9 21.2 + - - +
48F VAL* 3.5 31.8 - - + +
49F HIS* 3.6 15.2 + - + -
104G GLN* 1.6 63.5 + - + +
57H LYS* 4.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 2.9 48.1 + - - +
62E ILE* 4.0 3.4 - - - +
64E GLU* 1.3 78.9 - - + +
66E ALA* 1.3 60.9 + - - +
68E ASN* 3.3 13.4 + - + +
69E ALA* 3.1 22.2 + - - +
86E ALA* 3.8 20.9 - - + +
90E ASP* 4.9 12.1 - - + +
93E LEU* 4.3 15.5 - - + -
81G ARG* 5.8 4.3 - - - +
104G GLN* 3.6 21.1 - - - +
105G GLY 3.6 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE 2.9 20.4 + - - +
63E LEU* 3.6 7.2 - - - +
64E GLU 3.1 0.2 - - - -
65E LEU* 1.3 74.0 - - - +
67E GLY* 1.3 65.2 - - - +
69E ALA* 3.2 5.6 + - - +
70E ALA* 3.0 18.4 + - - +
78E ILE* 4.1 15.3 - - + -
82E HIS* 3.7 9.9 - - - +
83E LEU* 3.7 28.0 - - + +
86E ALA* 3.7 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU 2.9 14.9 + - - -
64E GLU 2.9 4.4 + - - -
66E ALA* 1.3 76.0 - - - +
68E ASN* 1.3 63.9 + - - +
70E ALA* 3.2 4.2 + - - +
71E ARG* 3.2 24.4 + - - +
78E ILE* 3.7 19.0 - - - +
49F HIS* 3.5 21.6 - - - -
52F THR* 4.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU* 2.9 13.0 + - - +
65E LEU* 3.4 20.1 - - + +
66E ALA 3.1 0.2 - - - -
67E GLY* 1.3 74.6 - - - +
69E ALA* 1.3 64.6 + - - +
71E ARG* 2.9 20.5 + - - +
72E ASP* 2.9 25.3 + - - +
49F HIS* 2.8 32.1 + - - -
79G ILE* 5.7 4.5 - - - +
81G ARG* 5.6 10.3 - - - +
104G GLN* 4.4 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU 3.1 9.9 + - - +
66E ALA 3.2 7.6 + - - +
68E ASN* 1.3 79.4 - - - +
70E ALA* 1.3 60.9 + - - +
72E ASP* 3.8 9.2 - - - +
73E ASN* 3.3 27.6 + - - +
82E HIS* 3.9 26.1 + - + +
85E LEU* 4.6 16.4 - - + -
86E ALA* 5.0 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ALA 3.0 10.5 + - - +
67E GLY* 3.4 11.4 - - - +
68E ASN 3.1 0.2 - - - -
69E ALA* 1.3 77.4 - - - +
71E ARG* 1.3 61.9 + - - +
73E ASN* 3.7 2.1 + - - +
74E LYS 3.5 3.3 + - - -
75E LYS* 3.0 34.1 + - - +
77E ARG 4.2 7.9 - - - +
78E ILE* 4.1 13.2 - - + -
82E HIS* 3.7 30.4 + - + +
52F THR* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLY 3.2 12.6 - - - +
68E ASN* 2.9 8.8 + - - +
70E ALA* 1.3 75.6 - - + +
72E ASP* 1.3 67.2 + - - +
73E ASN 3.0 2.6 + - - +
74E LYS* 3.3 15.0 + - - -
75E LYS 3.8 10.3 - - - +
49F HIS* 3.4 34.4 + - - +
50F PRO* 4.7 1.0 - - - +
51F ASP* 2.7 44.1 + - - -
52F THR* 3.3 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASN* 2.9 32.2 + - - +
69E ALA* 3.8 10.3 + - - +
71E ARG* 1.3 76.4 - - - +
73E ASN* 1.3 64.8 + - - +
73G ASN* 4.3 16.6 + - - -
81G ARG* 5.6 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASP* 4.3 15.6 + - - -
69E ALA* 3.3 15.7 + - - +
70E ALA 3.9 4.3 - - - +
71E ARG 3.0 2.3 + - - +
72E ASP* 1.3 85.4 - - - +
74E LYS* 1.4 66.6 + - + +
75E LYS* 4.5 7.3 - - + +
81E ARG* 5.7 2.8 - - - +
82E HIS* 4.2 18.2 - - + -
85E LEU* 4.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ALA 3.9 0.7 - - - -
71E ARG 3.3 7.5 + - - -
73E ASN* 1.4 82.7 - - + +
75E LYS* 1.3 70.2 + - + +
76E THR* 5.6 0.7 - - - +
----------------------------------------------------------
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