Contacts of the helix formed by residues 46 - 76 (chain E) in PDB entry 1VEQ
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 46 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN* 4.1 19.7 - - + +
155A HIS* 4.7 1.1 - - - -
45E PRO* 1.3 82.8 - - + +
47E PHE* 1.3 65.3 + - - +
48E ILE 3.7 1.1 - - - -
49E GLY* 3.6 11.3 + - - -
50E VAL* 3.8 9.2 + - - +
102E VAL* 3.6 32.3 - - - +
103E GLN* 4.7 4.4 + - - +
155E HIS* 4.4 4.2 + - - -
45L PRO* 2.8 36.2 + - - +
46L ASN* 4.2 12.0 - - + +
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Residues in contact with PHE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 4.1 14.6 - + - -
151A PHE* 3.1 34.8 - + - -
154A ALA* 3.7 20.9 - - + +
155A HIS* 3.2 35.8 + + + +
39E HIS 5.0 1.3 - - - -
42E VAL* 3.5 37.4 - - + +
44E GLY 3.6 16.5 + - - +
45E PRO 3.2 3.6 + - - -
46E ASN* 1.3 76.8 - - - +
48E ILE* 1.3 74.7 + - + +
49E GLY 3.1 1.0 + - - -
50E VAL* 3.1 3.3 + - - +
51E HIS* 3.0 54.0 + + + -
102E VAL* 4.7 7.0 - - - -
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Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 3.9 25.4 - - - +
53A MET* 3.1 43.7 - - + -
151A PHE* 4.1 28.0 - - + -
155A HIS* 3.5 12.1 + - + +
47E PHE* 1.3 81.5 - - + +
49E GLY* 1.3 72.0 + - - +
50E VAL 3.1 0.2 + - - -
51E HIS* 4.1 7.9 - - + -
52E GLU* 3.0 49.7 + - + +
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Residues in contact with GLY 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 5.1 6.8 - - - -
46E ASN* 3.6 9.6 + - - +
47E PHE 3.1 2.0 + - - -
48E ILE* 1.3 84.9 - - - +
50E VAL* 1.3 60.5 + - - +
52E GLU* 4.0 2.9 - - - +
53E MET* 3.1 20.8 + - - +
155E HIS* 5.5 0.7 - - - -
48L ILE* 4.1 23.3 - - - +
49L GLY* 5.3 5.4 - - - -
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Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E VAL* 5.4 0.7 - - + -
42E VAL* 4.6 13.5 - - + -
46E ASN* 3.8 6.4 + - - +
47E PHE 3.1 6.6 + - - +
49E GLY* 1.3 71.6 - - - +
51E HIS* 1.3 70.0 + - - +
53E MET* 2.7 30.8 + - + +
54E ILE* 3.1 30.9 + - + +
102E VAL* 3.2 34.8 - - + -
105E HIS* 6.5 0.4 - - + -
106E LEU* 3.9 20.9 - - + -
155E HIS* 4.0 17.9 - - + +
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Residues in contact with HIS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 4.4 6.7 - + - -
151A PHE* 3.7 26.7 - + - -
70B GLU* 3.2 23.6 + - - -
205B FE 4.1 0.8 - - - -
39E HIS* 2.7 78.4 + + - +
42E VAL* 5.4 3.1 - - - +
47E PHE* 3.0 38.0 + + + +
48E ILE* 3.5 15.9 - - + +
50E VAL* 1.3 81.9 - - - +
52E GLU* 1.3 67.4 - - + +
54E ILE* 3.6 10.6 + - - +
55E ASP 4.1 0.7 + - - -
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 6.0 1.4 - - - -
151A PHE* 6.1 0.2 - - - -
39E HIS* 5.1 2.5 - - + -
48E ILE* 3.0 39.1 + - + +
49E GLY 4.1 2.2 - - - +
51E HIS* 1.3 80.9 - - + +
53E MET* 1.3 65.2 + - - +
54E ILE 3.1 4.0 + - - -
55E ASP* 3.5 8.6 + - - +
56E PRO* 3.3 18.2 - - - +
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Residues in contact with MET 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLY 3.1 16.4 + - - +
50E VAL* 2.7 31.4 + - + +
52E GLU* 1.3 71.4 - - - +
54E ILE* 1.3 60.8 + - + +
56E PRO* 3.6 11.3 - - - +
57E GLN 4.5 1.9 + - - -
106E LEU* 4.1 26.7 - - + -
148E PHE* 4.1 29.1 - - + -
151E PHE* 4.0 20.6 - - + -
152E VAL* 4.7 1.8 - - - -
155E HIS* 3.8 16.2 - - + +
48L ILE* 3.3 38.8 - - + -
52L GLU* 6.1 0.9 - - - -
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Residues in contact with ILE 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 3.5 31.6 - - + +
38E VAL* 3.2 32.5 - - + +
39E HIS* 3.9 16.8 - - + -
42E VAL* 4.9 0.4 - - + -
50E VAL* 3.3 31.2 - - + +
51E HIS* 3.8 7.0 - - - +
52E GLU 3.1 0.8 - - - -
53E MET* 1.3 84.8 - - + +
55E ASP* 1.3 68.9 + - - +
56E PRO 3.3 0.9 - - - -
57E GLN* 3.0 14.4 + - - +
58E VAL* 3.1 26.7 + - + +
106E LEU* 6.1 0.9 - - + -
109E LEU* 5.5 3.1 - - + -
148E PHE* 4.7 8.5 - - + -
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Residues in contact with ASP 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B FE 3.9 4.2 - - - -
36E LYS* 3.1 29.3 + - - +
39E HIS* 3.2 27.3 + - - -
51E HIS 4.1 2.2 + - - +
52E GLU* 3.5 11.5 + - + +
54E ILE* 1.3 76.7 - - - +
56E PRO* 1.3 65.3 - - + +
58E VAL* 2.9 9.2 + - - +
59E GLU* 2.8 36.1 + - + +
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Residues in contact with PRO 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E GLU 3.3 14.1 - - - +
53E MET* 3.6 8.5 - - - +
54E ILE 3.5 3.1 - - - -
55E ASP* 1.3 94.1 - - + +
57E GLN* 1.3 55.9 + - - +
59E GLU* 3.2 7.8 + - + +
60E LEU* 2.8 33.5 + - + +
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 4.6 4.3 - - + -
53E MET 4.5 1.5 + - - +
54E ILE 3.0 7.9 + - - +
56E PRO* 1.3 78.3 - - - +
58E VAL* 1.3 56.7 - - - +
60E LEU* 3.5 19.6 - - - +
61E VAL* 2.9 43.9 + - + +
64E TYR* 5.6 1.0 - - - -
113E TYR* 3.1 29.2 + - - +
144E GLU* 4.2 5.7 + - - +
145E LEU* 3.5 27.5 - - - +
148E PHE* 3.0 59.0 - - + +
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.7 39.8 + - - +
32E HIS* 4.2 6.5 - - + +
35E LEU* 3.4 30.3 - - + -
36E LYS* 3.6 24.9 - - + +
54E ILE* 3.1 25.1 - - + +
55E ASP* 2.9 12.0 + - - +
57E GLN* 1.3 74.6 - - - +
59E GLU* 1.3 56.2 + - + +
60E LEU 2.7 13.3 + - - -
61E VAL* 3.0 6.1 + - - +
62E ARG* 2.9 24.3 + - - +
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Residues in contact with GLU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.6 31.7 - - - +
62B ARG* 3.8 19.6 + - - +
55E ASP* 2.8 23.1 + - + +
56E PRO* 3.6 7.2 - - + +
58E VAL* 1.3 72.3 - - + +
60E LEU* 1.3 57.3 + - - +
62E ARG* 4.2 4.8 - - - +
63E GLY* 3.5 13.9 + - - -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E PRO 2.8 18.0 + - - +
57E GLN* 3.5 19.5 - - - +
58E VAL 2.7 1.2 + - - -
59E GLU* 1.3 78.7 - - - +
61E VAL* 1.3 60.6 + - - +
62E ARG 3.2 1.3 - - - -
63E GLY* 2.8 18.4 + - - -
64E TYR* 3.0 43.6 + - + +
144E GLU* 3.5 33.7 - - + +
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Residues in contact with VAL 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 3.8 29.9 - - + +
31E LEU* 3.6 31.0 - - + -
32E HIS* 3.5 26.5 - - + -
35E LEU* 5.0 1.8 - - + -
57E GLN* 2.9 42.2 + - - +
58E VAL* 3.8 0.9 - - - +
60E LEU* 1.3 70.1 - - + +
62E ARG* 1.3 58.5 + - - +
63E GLY 2.9 4.5 - - - -
64E TYR* 2.8 28.3 + - + +
65E ALA* 3.1 10.6 + - - +
113E TYR* 4.4 2.2 - - - +
145E LEU* 4.6 4.9 - - + -
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 3.3 30.5 + - - -
36B LYS* 4.6 18.7 - - + +
58B VAL* 2.8 37.7 + - - +
59B GLU* 3.8 22.2 + - - +
62B ARG* 3.4 66.0 - - - +
32E HIS* 4.2 17.8 + - + +
58E VAL 2.9 8.3 + - - +
59E GLU* 4.4 7.0 - - - +
61E VAL* 1.3 78.5 - - - +
63E GLY* 1.3 60.8 + - - +
65E ALA* 3.2 22.2 + - + +
66E ASP* 3.4 8.3 + - - +
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Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLU 3.5 9.7 + - - -
60E LEU* 2.8 16.2 + - - -
62E ARG* 1.3 81.8 - - - +
64E TYR* 1.3 62.0 + - - +
66E ASP* 3.8 4.9 + - - +
67E GLU* 3.3 24.4 + - - +
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Residues in contact with TYR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 3.6 13.8 - + + -
57E GLN* 5.6 1.1 - - - -
60E LEU* 3.0 47.4 + - + +
61E VAL* 2.8 20.4 + - + +
63E GLY* 1.3 75.9 - - - +
65E ALA* 1.3 60.9 + - - +
67E GLU* 3.4 13.9 - - - -
68E VAL* 3.0 35.0 + - - +
140E ALA* 4.6 3.0 + - + -
141E HIS* 3.1 55.3 - + + +
144E GLU* 3.4 25.5 + - + +
145E LEU* 4.1 23.6 - - + -
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 6.2 1.1 - - + -
40B TRP* 4.1 14.1 - - + -
25E LEU* 4.4 5.2 - - + +
28E TYR* 4.5 12.8 - - + -
29E ASN* 4.3 20.2 - - - +
32E HIS* 5.1 1.6 - - + -
61E VAL 3.1 6.9 + - - +
62E ARG* 3.3 21.1 - - + +
63E GLY 3.1 0.4 - - - -
64E TYR* 1.3 75.0 - - - +
66E ASP* 1.3 68.8 + - - +
67E GLU 3.0 0.7 + - - -
68E VAL* 3.0 4.4 + - - +
69E ALA* 2.9 24.9 + - - +
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Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 2.9 27.8 + - - +
39B HIS* 3.0 9.4 + - - -
40B TRP* 3.1 17.6 + - - +
62E ARG 3.4 7.5 + - - +
63E GLY* 4.3 6.5 - - - +
65E ALA* 1.3 77.8 - - - +
67E GLU* 1.3 57.4 + - - +
70E GLU* 2.8 50.4 + - - +
202E FE 2.3 30.9 - - - -
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LYS* 5.2 8.2 + - - +
63E GLY 3.3 15.8 + - - +
64E TYR* 3.4 17.5 - - - +
65E ALA 3.0 0.6 + - - -
66E ASP* 1.3 80.1 + - - +
68E VAL* 1.3 61.4 + - - +
70E GLU* 4.0 4.2 - - - +
71E ARG* 3.2 21.5 + - - +
137E LEU* 4.7 18.2 - - + +
141E HIS* 3.0 27.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 3.6 43.3 - - + +
24E GLN* 4.7 4.9 - - + -
25E LEU* 4.3 14.4 - - + +
28E TYR* 3.7 22.0 - - + -
64E TYR 3.0 18.7 + - - +
65E ALA* 3.0 4.2 + - - +
67E GLU* 1.3 69.8 - - - +
69E ALA* 1.3 64.0 + - - +
71E ARG* 2.7 29.5 + - - +
72E ILE* 2.9 8.2 + - + +
137E LEU* 4.4 9.0 - - + -
138E LEU* 4.9 3.6 - - + -
141E HIS* 3.9 12.8 - - + -
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 3.2 38.4 - - + -
25E LEU* 3.2 29.1 - - + +
65E ALA 2.9 9.2 + - - +
68E VAL* 1.3 72.8 - - - +
70E GLU* 1.3 53.8 + - - +
71E ARG 2.7 1.6 + - - -
72E ILE* 2.7 27.7 + - - +
73E ALA* 3.1 10.0 + - - +
79E PRO* 3.4 14.9 - - + +
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 3.6 14.1 - - + -
51B HIS* 3.2 24.3 + - - -
147D LYS* 2.8 44.0 + - - +
150D TRP* 4.4 18.2 - - + -
151D PHE* 5.2 0.9 - - - -
66E ASP* 2.8 46.8 + - - +
67E GLU* 4.0 1.3 - - - +
69E ALA* 1.3 72.5 - - - +
71E ARG* 1.3 51.4 + - - +
73E ALA* 4.0 8.0 + - - +
74E THR* 2.5 32.4 + - - -
202E FE 2.2 27.5 - - - -
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Residues in contact with ARG 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ARG* 3.8 2.2 - - - +
143D GLY* 4.5 8.9 + - - -
146D GLU* 3.0 38.1 + - - +
147D LYS* 5.3 1.2 - - - +
6E ILE* 5.3 0.4 - - - -
21E LEU* 3.9 19.1 - - + -
67E GLU 3.2 13.9 + - - +
68E VAL* 2.7 17.6 + - - +
69E ALA 2.7 1.2 + - - -
70E GLU* 1.3 76.9 - - - +
72E ILE* 1.3 63.2 + - - +
74E THR* 3.1 28.5 + - - +
75E LEU* 3.1 23.2 + - + +
131E ASP* 2.8 28.9 + - - -
133E VAL* 3.5 23.5 - - - +
134E SER* 3.0 14.9 + - - +
137E LEU* 4.7 17.5 - - + -
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Residues in contact with ILE 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ALA* 4.5 9.9 - - + +
21E LEU* 3.7 21.8 - - + -
22E GLN* 3.5 45.5 - - + +
25E LEU* 4.5 3.8 - - + -
68E VAL* 2.9 17.5 + - + +
69E ALA* 2.7 22.9 + - - +
71E ARG* 1.3 70.5 - - - +
73E ALA* 1.3 64.1 + - - +
75E LEU* 2.8 26.6 + - - +
76E GLY 3.2 5.0 + - - -
77E LYS* 3.7 21.5 + - + +
78E SER 4.4 0.7 - - - -
79E PRO* 3.5 23.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 4.3 8.3 - - + +
99B ARG* 3.6 16.6 + - - +
150D TRP* 3.6 37.3 + - + +
4E PHE* 4.0 1.7 - - - -
69E ALA 3.1 8.4 + - - +
70E GLU* 4.2 2.7 - - - +
72E ILE* 1.3 78.6 - - - +
74E THR* 1.3 63.5 + - - +
76E GLY* 3.1 10.4 + - - -
77E LYS 3.4 12.8 - - - -
79E PRO* 3.7 15.7 - - + +
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Residues in contact with THR 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLU* 3.7 31.4 - - + +
147D LYS* 4.3 8.9 - - - +
149D GLN* 5.9 1.3 - - - +
150D TRP* 3.8 27.2 - - + +
153D ARG* 5.2 1.6 + - - -
4E PHE* 3.4 14.9 - - - -
6E ILE* 3.2 22.6 - - + +
70E GLU 2.5 24.3 + - - -
71E ARG* 3.1 22.6 + - - +
73E ALA* 1.3 79.7 - - - +
75E LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PHE* 3.9 0.8 - - - +
5E THR* 3.5 27.7 + - - -
6E ILE* 3.3 22.2 - - + -
9E LEU* 3.9 22.7 - - + -
14E ALA* 3.8 25.7 - - + +
17E VAL* 3.7 29.4 - - + -
18E ALA* 3.9 15.0 - - + +
21E LEU* 4.5 9.9 - - + -
71E ARG* 3.1 23.9 + - - +
72E ILE* 2.8 13.8 + - - +
74E THR* 1.3 80.4 - - - +
76E GLY* 1.3 55.2 + - - -
77E LYS 3.8 3.1 - - - +
131E ASP* 5.3 0.4 - - - +
134E SER* 4.8 2.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.1 24.7 + - - -
4E PHE* 4.1 21.8 - - - -
72E ILE 3.2 0.4 + - - -
73E ALA 3.1 11.5 + - - -
74E THR 3.3 0.2 - - - -
75E LEU* 1.3 80.1 - - - +
77E LYS* 1.3 67.1 + - - +
----------------------------------------------------------
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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