Contacts of the helix formed by residues 22 - 54 (chain H) in PDB entry 1F33
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 SER 22 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ASP 3.6 3.6 + - - -
21H VAL* 1.3 74.4 - - - +
23H ASP* 1.3 56.3 + - - +
24H SER* 3.6 10.9 - - - -
25H GLU* 3.0 32.2 + - - +
26H LYS* 2.8 31.7 + - - +
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Residues in contact with ASP 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H THR* 3.3 25.4 + - - +
14H LEU* 3.9 21.5 - - + +
21H VAL 3.4 3.9 + - - +
22H SER* 1.3 71.9 - - - +
24H SER* 1.3 63.3 + - - +
26H LYS* 4.0 6.9 + - - +
27H LYS* 2.9 32.0 + - + +
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Residues in contact with SER 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H SER* 3.6 11.2 - - - -
23H ASP* 1.3 80.0 - - - +
25H GLU* 1.3 59.8 + - - +
27H LYS* 3.9 3.3 - - - +
28H ALA* 3.0 27.1 + - - +
140H LYS* 4.3 12.1 + - - -
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Residues in contact with GLU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H VAL* 3.7 18.3 - - + +
22H SER* 3.0 19.4 + - - +
24H SER* 1.3 78.3 - - - +
26H LYS* 1.3 58.2 + - - +
28H ALA* 4.1 6.3 - - - -
29H THR* 2.6 43.9 + - - +
140H LYS* 3.1 46.1 - - + +
141H ASP* 3.4 15.2 + - - +
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Residues in contact with LYS 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.4 25.7 - - + +
15H LEU 5.2 2.0 + - - -
17H THR* 3.4 24.0 + - - +
19H ASN* 2.8 32.2 + - - -
20H ASP* 4.8 0.2 - - - +
21H VAL* 2.9 38.2 + - + +
22H SER 2.8 21.6 + - - +
23H ASP* 3.7 7.0 + - - +
25H GLU* 1.3 72.2 - - - +
27H LYS* 1.3 58.0 + - - +
29H THR* 3.7 2.0 - - - -
30H VAL* 2.8 37.6 + - - +
87H LEU* 3.2 33.4 - - + +
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Residues in contact with LYS 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H THR* 3.0 28.2 + - - +
13H ASN* 3.2 29.9 - - - +
14H LEU* 3.6 21.1 - - + -
23H ASP* 2.9 21.4 + - + +
24H SER* 3.9 3.4 - - - +
26H LYS* 1.3 75.5 - - - +
28H ALA* 1.3 62.9 + - - +
30H VAL* 3.5 3.7 + - - +
31H GLU* 3.1 24.9 + - - +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H SER 3.0 17.5 + - - +
25H GLU* 3.6 3.8 - - - +
27H LYS* 1.3 76.8 - - - +
29H THR* 1.3 63.5 + - - +
31H GLU* 3.2 10.3 + - - +
32H LEU* 3.0 22.5 + - - +
140H LYS* 3.9 30.3 - - + +
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Residues in contact with THR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H VAL* 5.7 0.2 - - - +
25H GLU* 2.6 31.6 + - - +
28H ALA* 1.3 71.0 - - - +
30H VAL* 1.3 59.8 + - - +
32H LEU* 3.0 8.8 + - + +
33H LEU* 2.8 39.0 + - + +
87H LEU* 3.3 24.5 - - + +
140H LYS* 5.3 3.6 + - - +
141H ASP* 3.8 17.9 + - - +
144H THR* 3.1 36.3 - - + +
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Residues in contact with VAL 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 4.4 5.8 - - + -
26H LYS 2.8 32.4 + - - +
27H LYS* 3.8 6.7 - - - +
29H THR* 1.3 71.6 - - - +
31H GLU* 1.3 58.6 + - - +
33H LEU* 3.6 1.5 + - - +
34H ASN* 3.0 46.3 + - - +
84H ALA* 3.7 33.4 - - + +
87H LEU* 4.1 9.0 - - + -
89H GLY* 3.7 28.9 - - - +
90H VAL 4.2 2.2 - - - +
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LYS 3.1 13.4 + - - +
28H ALA* 3.4 12.2 - - - +
29H THR 3.1 0.6 - - - -
30H VAL* 1.3 76.9 - - - +
32H LEU* 1.3 65.7 + - - +
34H ASN* 4.0 4.9 - - - +
35H ARG* 3.1 26.6 + - + +
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Residues in contact with LEU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ALA 3.0 12.6 + - - +
29H THR* 3.0 11.8 + - + +
31H GLU* 1.3 78.0 - - - +
33H LEU* 1.3 62.2 + - + +
35H ARG* 3.2 51.4 + - - +
36H GLN* 3.2 10.4 + - + +
135H ALA* 3.9 32.5 - - + +
138H GLU* 3.6 20.4 - - + +
139H ALA* 4.0 23.3 - - + +
144H THR* 5.1 4.7 - - + -
148H LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H THR* 2.8 29.6 + - + +
30H VAL 3.9 3.4 - - - +
32H LEU* 1.3 74.4 - - - +
34H ASN* 1.3 60.7 + - - +
36H GLN* 2.8 9.0 + - - +
37H VAL* 2.8 30.8 + - - +
80H MET* 3.6 32.9 - - + +
83H ARG* 3.5 21.5 - - + -
84H ALA* 3.4 37.0 - - + +
144H THR* 3.5 26.0 - - + -
147H ILE* 5.2 2.5 - - + -
148H LEU* 4.6 10.3 - - + -
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Residues in contact with ASN 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H VAL* 3.0 38.3 + - - +
31H GLU* 4.1 5.3 - - - +
32H LEU 3.5 0.2 - - - -
33H LEU* 1.3 75.7 - - - +
35H ARG* 1.3 61.9 + - - +
37H VAL* 3.7 8.5 - - - +
38H ILE* 3.1 33.6 + - + +
84H ALA* 4.5 5.0 - - - +
90H VAL 3.0 21.7 + - - -
91H ALA* 3.3 5.8 - - - +
92H LEU* 2.6 49.0 + - + +
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Residues in contact with ARG 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H GLU* 3.1 18.2 + - - +
32H LEU* 3.2 38.8 - - - +
33H LEU 3.0 0.6 - - - -
34H ASN* 1.3 78.9 - - - +
36H GLN* 1.3 70.7 + - - +
38H ILE* 3.6 9.9 + - - +
39H GLN* 3.4 22.9 + - - +
103H PRO* 5.7 1.2 - - - +
131H ASP* 2.9 40.0 + - - -
135H ALA* 4.3 3.8 - - - +
138H GLU* 3.9 14.3 + - - -
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Residues in contact with GLN 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.5 16.2 - - + +
33H LEU* 2.8 8.3 + - - +
35H ARG* 1.3 84.1 + - - +
37H VAL* 1.3 59.4 + - - +
39H GLN* 2.8 28.4 + - - +
40H PHE* 2.8 53.3 + - - -
80H MET* 3.6 19.3 - - + -
131H ASP* 3.6 14.9 - - - +
132H VAL* 3.6 16.5 - - - +
135H ALA* 3.6 20.8 - - - +
148H LEU* 3.9 18.6 - - + -
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G TRP* 4.6 7.0 - - + -
33H LEU 2.8 22.7 + - - +
34H ASN* 3.7 14.1 - - - +
36H GLN* 1.3 71.7 - - - +
38H ILE* 1.3 58.1 + - - +
40H PHE* 3.3 2.2 + - - +
41H ILE* 2.9 53.2 + - + +
77H LEU* 3.9 16.8 - - + +
80H MET* 4.0 12.1 - - + +
81H ALA* 3.8 32.8 - - + +
92H LEU 3.6 21.5 - - - +
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Residues in contact with ILE 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ASN* 3.1 21.9 + - + +
35H ARG* 3.8 8.3 - - - +
36H GLN 3.2 0.2 - - - -
37H VAL* 1.3 76.3 - - - +
39H GLN* 1.3 62.3 + - - +
42H ASP* 3.1 23.6 + - - +
92H LEU* 4.0 18.4 - - + +
97H VAL* 3.6 22.9 - - + -
98H ILE* 3.5 38.1 - - + +
101H LYS* 4.0 42.8 - - + +
102H THR* 4.1 6.3 - - - -
103H PRO* 5.0 0.7 - - + -
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Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ARG* 3.4 11.1 + - - +
36H GLN* 2.8 37.1 + - - +
38H ILE* 1.3 80.6 - - - +
40H PHE* 1.3 56.9 + - + +
42H ASP* 3.5 4.4 + - - +
43H LEU* 3.0 28.6 + - - +
103H PRO* 3.3 38.6 - - + +
104H LEU* 4.0 3.9 - - + +
127H ILE* 4.3 6.7 - - - +
128H VAL* 3.4 37.5 - - + +
131H ASP* 3.0 35.4 + - - +
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Residues in contact with PHE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLN* 2.8 50.9 + - - +
37H VAL 3.8 2.9 - - - +
39H GLN* 1.3 70.6 - - - +
41H ILE* 1.3 66.6 - - - +
43H LEU* 3.2 7.2 + - - +
44H SER* 2.8 25.3 + - - -
73H LEU* 3.8 30.9 - - + +
76H HIS* 4.0 15.7 - + + -
77H LEU* 4.1 16.4 - - + -
80H MET* 3.7 23.1 - - + -
128H VAL* 3.6 19.5 - - + -
132H VAL* 4.3 9.0 - - + -
151H ALA* 3.9 14.4 - - + -
155H LEU* 3.2 34.1 - - + -
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Residues in contact with ILE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LEU* 3.7 28.3 - - + -
52G TRP* 4.4 6.1 - - + -
37H VAL* 2.9 33.6 + - + +
40H PHE* 1.3 75.1 - - - +
42H ASP* 1.3 62.5 + - - +
44H SER* 2.7 21.2 + - - +
45H LEU* 3.0 17.8 + - + +
77H LEU* 3.2 30.7 - - + -
93H GLY* 3.6 34.1 - - - +
98H ILE* 3.9 20.4 - - + -
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Residues in contact with ASP 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G THR* 3.0 36.6 + - - +
96G GLN* 4.7 1.6 - - - +
38H ILE 3.1 18.3 + - - +
39H GLN 3.8 4.0 - - - +
41H ILE* 1.3 78.2 - - - +
43H LEU* 1.3 56.9 + - - +
45H LEU* 3.2 5.9 + - - +
46H ILE* 2.9 43.3 + - - +
98H ILE* 3.8 9.8 - - + +
102H THR* 2.6 31.2 + - - +
104H LEU* 3.3 20.2 - - + +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN 3.0 18.3 + - - +
40H PHE* 3.2 6.5 + - + +
42H ASP* 1.3 76.3 - - - +
44H SER* 1.3 53.2 + - - +
46H ILE* 3.4 7.6 + - + +
47H THR* 2.6 36.7 + - - -
73H LEU* 4.1 11.0 - - + -
104H LEU* 3.9 11.8 - - + +
124H ARG* 3.8 27.1 - - + +
125H TYR* 3.5 45.1 - - + -
128H VAL* 4.0 11.7 - - + -
155H LEU* 3.8 29.4 - - + -
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Residues in contact with SER 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H PHE 2.8 14.6 + - - -
41H ILE* 2.7 25.1 + - - +
43H LEU* 1.3 72.7 - - - +
45H LEU* 1.3 69.3 + - - +
47H THR* 3.2 5.7 + - - -
48H LYS* 3.2 24.1 + - - +
70H ARG* 4.1 16.5 + - - +
73H LEU* 3.8 26.4 - - - +
74H ILE* 4.6 13.1 - - - +
77H LEU* 4.7 2.6 - - - +
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ILE* 3.6 31.2 - - + -
45G LEU* 4.7 18.6 - - + -
93G GLY 3.8 18.1 - - - +
94G THR* 4.9 1.3 - - - -
95G THR* 4.0 34.8 - - - +
98G ILE* 5.3 1.6 - - + -
41H ILE* 3.0 25.4 + - + +
42H ASP* 3.5 10.1 - - - +
44H SER* 1.3 84.5 + - - +
46H ILE* 1.3 64.4 - - + +
48H LYS* 3.2 9.3 + - + +
49H GLN* 3.1 21.2 + - - +
52H TRP* 5.2 0.7 - - - -
98H ILE* 5.2 2.5 - - + -
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Residues in contact with ILE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G THR* 5.2 6.3 - - + -
96G GLN* 5.8 3.4 - - - +
42H ASP* 2.9 34.9 + - - +
43H LEU* 3.6 7.0 - - + +
45H LEU* 1.3 74.0 - - + +
47H THR* 1.3 65.1 + - - +
49H GLN* 3.0 18.1 + - - +
50H ALA* 3.1 13.5 + - - +
104H LEU* 3.7 32.1 - - + -
105H LYS 4.8 2.0 - - - +
107H TYR* 3.4 40.8 - - + +
121H LEU* 3.9 11.2 - - + -
124H ARG* 4.2 22.9 - - + +
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Residues in contact with THR 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU 2.6 27.4 + - - -
44H SER* 3.2 8.7 + - - -
46H ILE* 1.3 75.3 - - - +
48H LYS* 1.3 59.2 + - - +
50H ALA* 3.6 2.6 + - - +
51H HIS* 3.0 28.5 + - + +
66H LEU* 3.3 44.6 - - + +
70H ARG* 4.5 10.3 - - + +
73H LEU* 3.8 3.9 - - - +
121H LEU* 4.3 9.4 - - - -
125H TYR* 2.7 31.7 + - + +
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Residues in contact with LYS 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ASP* 2.8 25.5 + - - +
82G GLU* 5.5 1.0 + - - -
44H SER 3.2 9.7 + - - +
45H LEU* 3.2 11.3 + - - +
46H ILE 3.1 0.2 - - - -
47H THR* 1.3 80.1 - - + +
49H GLN* 1.3 59.0 + - - +
51H HIS* 3.1 35.1 + - + +
52H TRP* 2.9 66.7 + - + +
67H ASP* 2.9 22.4 + - - +
70H ARG* 3.0 48.0 - - + +
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Residues in contact with GLN 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G VAL* 5.3 0.8 - - - +
91G ALA 2.6 24.6 + - - +
92G LEU* 3.2 4.0 - - - +
93G GLY* 3.0 19.2 + - - +
94G THR* 3.2 36.8 - - + +
45H LEU 3.1 8.7 + - - +
46H ILE* 3.0 14.0 + - - +
48H LYS* 1.3 77.3 - - - +
50H ALA* 1.3 62.5 + - - +
52H TRP* 4.0 5.3 - - - -
53H ASN* 2.9 47.7 + - - +
107H TYR* 4.2 15.2 - - + -
108H PRO 4.5 3.8 + - - -
109H LEU* 4.1 20.4 - - - +
117H HIS* 4.5 1.4 - - - -
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE 3.1 4.6 + - - +
47H THR 3.9 1.1 - - - +
49H GLN* 1.3 78.5 - - - +
51H HIS* 1.3 65.7 + - - +
53H ASN 3.3 1.7 + - - -
54H MET* 3.2 32.4 + - + +
107H TYR* 3.4 22.4 - - - +
117H HIS* 3.4 19.6 - - + +
121H LEU* 3.6 35.2 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G GLU* 4.8 5.3 + - - -
47H THR* 3.0 20.7 + - + +
48H LYS* 3.1 38.2 + - + +
50H ALA* 1.3 78.1 - - - +
52H TRP* 1.3 79.8 + + - +
54H MET* 3.5 10.0 - - - +
59H PHE* 4.6 0.7 - - - -
63H HIS* 2.6 83.3 + + - -
64H GLU* 4.9 0.4 - - - -
66H LEU* 3.9 17.0 - - + +
67H ASP* 3.8 21.8 + - + +
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Residues in contact with TRP 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G VAL* 4.6 2.5 - - + -
41G ILE* 4.3 11.2 - - + -
77G LEU* 3.6 20.6 - - + -
78G ASP* 3.3 31.6 + - - +
81G ALA* 3.4 26.2 - - + +
82G GLU* 4.3 16.3 + - + +
85G VAL* 3.5 25.2 - - + +
91G ALA* 3.9 24.0 - - + -
92G LEU 4.8 0.7 - - - -
93G GLY* 4.1 24.5 - - - -
45H LEU 5.2 0.2 - - - -
48H LYS* 2.9 54.3 + - + +
49H GLN* 4.0 7.6 - - - -
51H HIS* 1.3 97.2 - + - +
53H ASN* 1.3 68.2 + - - +
54H MET 3.5 3.0 + - - +
63H HIS* 4.6 3.1 - + - -
160I TRP* 3.9 10.4 - + + -
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Residues in contact with ASN 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL* 3.5 13.7 - - - +
89G GLY 4.3 1.0 - - - +
90G VAL* 3.5 16.0 - - + +
91G ALA* 3.0 44.3 + - - +
49H GLN* 2.9 33.9 + - - +
50H ALA 3.3 3.2 + - - -
52H TRP* 1.3 81.9 - - - +
54H MET* 1.3 59.5 + - - +
55H ARG* 4.8 2.8 - - - +
111H ILE 4.6 1.6 - - - +
112H HIS* 3.1 33.4 + - + +
117H HIS* 3.3 19.5 + - + +
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Residues in contact with MET 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL* 6.1 0.2 - - - +
50H ALA 3.2 17.8 + - - +
51H HIS 3.5 11.2 - - - +
52H TRP 3.5 3.4 - - - +
53H ASN* 1.3 79.1 - - - +
55H ARG* 1.3 68.5 + - - +
59H PHE* 3.3 32.7 - - + +
62H VAL* 3.5 28.7 - - + -
63H HIS* 4.1 13.2 - - - -
66H LEU* 3.3 30.5 - - + -
112H HIS 3.2 5.6 - - - +
114H VAL* 4.3 16.6 - - + +
117H HIS* 3.7 27.8 - - + -
118H LEU* 5.0 0.9 - - + -
121H LEU* 4.7 2.0 - - + -
160I TRP* 5.3 1.4 + - - -
164I SER* 4.5 1.2 + - - -
----------------------------------------------------------
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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