Contacts of the helix formed by residues 22 - 53 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ASP 3.6 2.8 + - - -
21F VAL* 1.3 75.8 - - - +
23F ASP* 1.3 65.7 + - - +
24F SER* 2.8 11.6 - - - -
25F GLU* 3.0 32.6 + - - +
26F LYS* 2.8 20.8 + - - +
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Residues in contact with ASP 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F THR* 3.4 35.2 - - - +
14F LEU* 3.9 14.7 - - + +
21F VAL 3.4 3.7 + - - +
22F SER* 1.3 72.2 - - - +
24F SER* 1.3 57.8 + - - +
26F LYS* 3.7 5.4 + - - +
27F LYS* 2.8 36.7 + - + +
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Residues in contact with SER 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER* 2.8 12.3 - - - -
23F ASP* 1.3 80.2 - - - +
25F GLU* 1.3 59.4 + - - +
27F LYS* 3.3 5.5 - - - +
28F ALA* 3.0 26.7 + - - +
140F LYS* 4.2 12.2 + - - -
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Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F VAL* 3.7 17.3 - - + +
22F SER* 2.9 18.8 + - - +
24F SER* 1.3 79.6 - - - +
26F LYS* 1.3 57.8 + - - +
28F ALA* 4.2 6.3 - - - -
29F THR* 2.6 44.1 + - - +
140F LYS* 3.1 43.3 - - + +
141F ASP* 3.4 16.9 + - + +
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 3.5 26.2 - - + +
15F LEU 5.1 2.6 + - - -
17F THR* 3.3 25.0 + - - +
19F ASN* 2.9 30.4 + - - -
21F VAL* 2.9 42.5 + - + +
22F SER 2.8 13.5 + - - +
23F ASP* 4.4 6.3 + - - -
25F GLU* 1.3 71.5 - - - +
27F LYS* 1.3 54.7 + - - +
29F THR* 3.7 0.3 - - - -
30F VAL* 2.7 42.1 + - - +
87F LEU* 3.1 37.9 - - + +
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Residues in contact with LYS 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ALA 4.3 6.7 + - - -
12F THR* 3.5 22.8 - - - +
13F ASN* 3.4 37.3 - - - +
14F LEU* 4.3 10.7 - - + +
23F ASP 2.8 22.5 + - - +
24F SER* 3.3 7.0 - - - +
26F LYS* 1.3 79.1 - - - +
28F ALA* 1.3 60.9 + - - +
30F VAL* 3.7 4.1 + - - +
31F GLU* 3.4 20.7 + - - +
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F SER 3.0 13.4 + - - +
25F GLU* 3.6 3.8 - - - +
27F LYS* 1.3 78.1 - - - +
29F THR* 1.3 58.3 + - - +
31F GLU* 3.3 9.6 + - - +
32F LEU* 3.0 27.3 + - - +
140F LYS* 3.8 31.2 - - + +
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Residues in contact with THR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLU* 2.6 31.7 + - - +
28F ALA* 1.3 70.6 - - - +
30F VAL* 1.3 66.7 + - - +
32F LEU* 3.0 8.5 + - - +
33F LEU* 2.9 32.0 + - + +
87F LEU* 3.3 24.1 - - + +
140F LYS* 5.2 4.2 + - - +
141F ASP* 3.8 18.7 + - + +
144F THR* 3.1 36.8 - - + +
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Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 4.5 5.8 - - + -
26F LYS 2.7 28.5 + - - +
27F LYS* 3.9 5.6 - - - +
29F THR* 1.3 72.6 - - - +
31F GLU* 1.3 58.9 + - - +
33F LEU* 3.8 1.5 - - - +
34F ASN* 3.0 47.1 + - - +
84F ALA* 3.6 32.9 - - + +
87F LEU* 4.2 10.1 - - + -
89F GLY* 3.6 28.3 - - - +
90F VAL 4.2 2.7 - - - +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LYS 3.4 11.9 + - - +
28F ALA* 3.3 11.8 + - - +
29F THR 3.1 0.6 - - - -
30F VAL* 1.3 78.9 - - - +
32F LEU* 1.3 66.1 + - - +
34F ASN* 4.1 4.9 - - - +
35F ARG* 3.2 27.7 + - + +
101F LYS* 6.2 2.5 - - - +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ALA 3.0 12.2 + - - +
29F THR* 3.0 11.7 + - + +
31F GLU* 1.3 78.3 - - - +
33F LEU* 1.3 62.3 + - + +
35F ARG* 3.3 37.4 - - - +
36F GLN* 3.2 20.3 + - + +
135F ALA* 3.9 32.1 - - + +
138F GLU* 3.7 20.6 - - + +
139F ALA* 4.0 23.1 - - + +
144F THR* 5.0 4.7 - - + -
148F LEU* 4.2 12.3 - - + -
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F THR* 2.9 32.9 + - + +
30F VAL 3.8 3.1 - - - +
32F LEU* 1.3 75.6 - - - +
34F ASN* 1.3 60.7 + - - +
36F GLN* 2.8 8.4 + - - +
37F VAL* 2.8 30.8 + - - +
80F MET* 3.6 32.3 - - + +
83F ARG* 3.5 21.3 - - + +
84F ALA* 3.4 37.0 - - + +
144F THR* 3.5 23.3 - - + -
147F ILE* 5.2 2.2 - - + -
148F LEU* 4.5 10.3 - - + -
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Residues in contact with ASN 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F VAL* 3.0 39.3 + - - +
31F GLU* 4.1 4.9 - - - +
33F LEU* 1.3 76.4 - - - +
35F ARG* 1.3 61.5 + - - +
37F VAL* 3.6 8.4 - - - +
38F ILE* 3.0 34.7 + - + +
84F ALA* 4.5 5.0 - - - +
90F VAL 3.0 21.2 + - - -
91F ALA* 3.3 5.8 - - - +
92F LEU* 2.6 48.9 + - + +
101F LYS* 6.0 2.7 - - - +
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Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLU* 3.2 17.6 + - - +
32F LEU* 3.3 37.9 - - - +
33F LEU 3.0 0.4 - - - -
34F ASN* 1.3 77.3 - - - +
36F GLN* 1.3 71.6 + - - +
38F ILE* 3.6 9.0 + - - +
39F GLN* 3.4 23.0 + - - +
101F LYS* 6.3 0.9 - - - +
131F ASP* 2.9 40.8 + - - -
135F ALA* 4.3 4.2 - - - +
138F GLU* 3.8 14.8 + - - -
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Residues in contact with GLN 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.2 17.2 + - + +
33F LEU* 2.8 7.9 + - - +
35F ARG* 1.3 83.5 + - - +
37F VAL* 1.3 59.6 + - - +
39F GLN* 2.9 26.3 + - - +
40F PHE* 2.8 53.7 + - - -
80F MET* 3.6 18.8 - - + -
131F ASP* 3.7 10.7 - - - +
132F VAL* 3.6 22.2 - - - +
135F ALA* 3.6 20.4 - - - +
148F LEU* 4.0 17.9 - - + -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E TRP* 4.6 6.7 - - + -
33F LEU 2.8 23.4 + - - +
34F ASN* 3.6 14.8 - - - +
36F GLN* 1.3 73.5 - - - +
38F ILE* 1.3 57.8 + - - +
40F PHE* 3.7 1.9 - - - +
41F ILE* 2.8 53.0 + - + +
77F LEU* 4.0 17.0 - - + +
80F MET* 4.0 11.6 - - + +
81F ALA* 3.8 32.5 - - + +
84F ALA* 6.2 0.2 - - + -
91F ALA* 5.8 0.2 - - + -
92F LEU 3.6 21.5 - - - +
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Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ASN* 3.0 20.8 + - + +
35F ARG* 3.8 8.1 - - - +
37F VAL* 1.3 76.1 - - - +
39F GLN* 1.3 64.3 + - - +
41F ILE 3.5 0.2 + - - -
42F ASP* 3.1 23.7 + - - +
92F LEU* 4.1 15.3 - - + +
97F VAL* 3.6 24.2 - - + -
98F ILE* 3.5 40.9 - - + +
101F LYS* 3.8 28.9 - - + +
102F THR* 4.0 23.6 - - - +
103F PRO* 5.0 1.1 - - + -
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ARG* 3.4 11.6 + - - +
36F GLN* 2.9 32.8 + - - +
38F ILE* 1.3 80.1 - - - +
40F PHE* 1.3 57.8 + - + +
42F ASP* 3.4 5.6 + - - +
43F LEU* 2.9 30.0 + - - +
102F THR* 5.3 0.2 - - - -
103F PRO* 3.4 37.0 - - + +
104F LEU* 4.0 3.4 - - + +
127F ILE* 4.3 6.7 - - - +
128F VAL* 3.4 36.7 - - + +
131F ASP* 3.0 35.8 + - - +
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Residues in contact with PHE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLN* 2.8 50.9 + - - +
37F VAL 3.8 3.1 - - - +
39F GLN* 1.3 70.6 - - + +
41F ILE* 1.3 66.5 + - - +
43F LEU* 3.2 7.3 + - + +
44F SER* 2.9 24.9 + - - -
73F LEU* 3.9 29.7 - - + +
76F HIS* 4.0 7.4 - - + -
77F LEU* 4.1 16.3 - - + +
80F MET* 3.6 22.0 - - + -
128F VAL* 3.6 18.2 - - + -
132F VAL* 4.3 8.5 - - + -
151F ALA* 3.9 21.3 - - + -
155F LEU* 3.2 35.0 - - + -
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Residues in contact with ILE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 3.6 28.5 - - + -
52E TRP* 4.3 11.2 - - + -
37F VAL* 2.8 42.2 + - + +
38F ILE 3.9 3.6 - - - +
40F PHE* 1.3 72.4 - - - +
42F ASP* 1.3 62.9 + - - +
44F SER* 2.6 21.9 + - - +
45F LEU* 3.0 16.7 + - + +
77F LEU* 3.3 25.1 - - + -
93F GLY* 3.7 27.6 - - - +
98F ILE* 3.9 15.9 - - + -
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E THR* 3.0 36.2 + - - +
96E GLN* 4.8 1.6 - - - +
38F ILE 3.1 17.9 + - - +
39F GLN 3.8 3.4 - - - +
41F ILE* 1.3 77.6 - - - +
43F LEU* 1.3 58.2 + - - +
45F LEU* 3.1 7.1 + - - +
46F ILE* 2.9 42.7 + - - +
98F ILE* 3.7 8.9 - - + +
102F THR* 2.6 32.6 + - - +
104F LEU* 3.4 19.4 - - + +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN 2.9 18.2 + - - +
40F PHE* 3.2 6.9 + - - +
42F ASP* 1.3 76.3 - - - +
44F SER* 1.3 52.2 + - - +
46F ILE* 3.3 7.7 + - + +
47F THR* 2.7 37.0 + - - -
73F LEU* 4.1 10.3 - - + -
104F LEU* 3.8 12.5 - - + +
124F ARG* 3.8 27.8 - - + +
125F TYR* 3.5 46.7 - - + -
128F VAL* 3.9 11.9 - - + -
155F LEU* 3.8 28.0 - - + -
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Residues in contact with SER 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE 2.9 13.3 + - - -
41F ILE* 2.6 25.2 + - - +
43F LEU* 1.3 74.0 - - - +
45F LEU* 1.3 69.1 + - - +
47F THR* 3.4 5.5 + - - -
48F LYS* 3.3 23.9 + - - +
70F ARG* 4.1 16.8 - - - +
73F LEU* 3.9 25.7 - - - +
74F ILE* 4.6 13.9 - - - +
77F LEU* 4.7 2.2 - - - +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ILE* 3.6 31.4 - - + -
45E LEU* 4.7 19.3 - - + -
93E GLY 3.8 19.2 - - - +
94E THR* 5.0 1.1 - - - -
95E THR* 4.1 34.5 - - - +
98E ILE* 5.3 1.8 - - + -
41F ILE* 3.0 24.9 + - + +
42F ASP* 3.1 11.6 + - - +
44F SER* 1.3 85.0 + - - +
46F ILE* 1.3 63.6 + - - +
48F LYS* 3.2 8.8 + - + +
49F GLN* 3.1 19.8 + - - +
52F TRP* 5.2 0.3 - - - -
98F ILE* 5.2 2.2 - - + -
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E THR* 5.2 6.7 - - + -
96E GLN* 5.8 2.9 - - - +
42F ASP* 2.9 32.2 + - - +
43F LEU* 3.5 8.1 - - + +
45F LEU* 1.3 76.6 - - + +
47F THR* 1.3 66.1 + - - +
49F GLN* 3.0 18.2 + - - +
50F ALA* 3.0 13.2 + - - +
104F LEU* 3.8 30.3 - - + +
105F LYS 4.7 2.2 - - - +
107F TYR* 3.4 41.1 - - + +
121F LEU* 3.8 11.9 - - + -
124F ARG* 4.1 24.0 - - + +
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LEU 2.7 25.9 + - - -
44F SER* 3.4 9.0 - - - -
46F ILE* 1.3 75.1 - - - +
48F LYS* 1.3 59.5 + - + +
50F ALA* 3.6 2.8 + - - +
51F HIS* 3.0 28.1 + - - +
66F LEU* 3.3 44.1 - - + +
67F ASP* 5.4 0.2 - - - -
70F ARG* 4.4 10.3 - - + +
73F LEU* 3.8 3.1 - - - +
121F LEU* 4.3 9.6 - - - -
125F TYR* 2.7 32.1 + - + +
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Residues in contact with LYS 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ASP* 2.8 22.7 + - - +
82E GLU* 5.4 1.2 + - - -
44F SER 3.3 9.3 + - - +
45F LEU* 3.2 11.5 + - + +
46F ILE 3.2 0.6 - - - -
47F THR* 1.3 78.8 - - + +
49F GLN* 1.3 56.0 + - - +
51F HIS* 3.1 33.6 + - + +
52F TRP* 2.8 69.9 + - + +
67F ASP* 2.8 24.9 + - - +
70F ARG* 2.9 48.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E VAL* 5.3 1.2 - - - +
91E ALA 2.6 23.7 + - - +
92E LEU* 3.2 4.0 - - - +
93E GLY* 3.0 20.0 + - - +
94E THR* 3.2 38.1 - - + +
45F LEU 3.1 9.0 + - - +
46F ILE* 3.0 13.4 + - - +
48F LYS* 1.3 78.6 - - - +
50F ALA* 1.3 61.7 + - - +
52F TRP* 3.9 5.6 - - - -
53F ASN* 2.9 47.8 + - - +
107F TYR* 4.3 15.4 - - + -
108F PRO 4.4 4.2 + - - -
109F LEU* 4.0 18.7 - - - +
117F HIS* 5.4 1.0 - - - -
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Residues in contact with ALA 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE 3.0 7.2 + - - +
47F THR 3.9 1.1 - - - +
49F GLN* 1.3 76.6 - - - +
51F HIS* 1.3 64.0 + - - +
53F ASN 3.3 2.1 + - - -
54F MET* 3.2 31.7 + - + +
107F TYR* 3.3 23.3 - - - +
117F HIS* 3.5 18.3 - - + +
121F LEU* 3.6 35.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E GLU* 4.7 5.7 + - - -
47F THR* 3.0 21.0 + - + +
48F LYS* 3.1 37.3 + - + +
50F ALA* 1.3 79.0 - - - +
52F TRP* 1.3 80.1 + + - +
54F MET* 3.6 9.6 - - - +
59F PHE* 4.6 0.7 - - - -
63F HIS* 2.6 81.9 + + - -
64F GLU* 5.0 0.4 - - - -
66F LEU* 3.9 18.1 - - + +
67F ASP* 3.8 20.5 + - + -
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Residues in contact with TRP 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 3.9 9.4 - + - -
37E VAL* 4.6 2.5 - - + -
41E ILE* 4.3 11.0 - - + -
77E LEU* 3.6 20.4 - - + -
78E ASP* 3.4 30.3 + - - +
81E ALA* 3.3 27.0 - - + +
82E GLU* 4.3 16.3 - - + +
85E VAL* 3.5 25.0 - - + +
91E ALA* 3.9 29.2 - - + -
92E LEU 4.8 0.9 - - - -
93E GLY* 4.1 23.3 - - - -
45F LEU 5.2 0.7 - - - -
48F LYS* 2.8 52.9 + - + +
49F GLN* 3.9 7.6 - - - -
51F HIS* 1.3 95.1 + + - +
53F ASN* 1.3 62.4 + - - +
54F MET 3.5 2.8 + - - +
63F HIS* 4.6 3.1 - + - -
----------------------------------------------------------
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Residues in contact with ASN 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL* 3.5 14.6 - - - +
89E GLY 4.3 1.0 - - - +
90E VAL* 3.5 14.8 - - + +
91E ALA 2.9 44.9 + - - +
49F GLN* 2.9 33.5 + - - +
50F ALA 3.3 4.8 + - - -
52F TRP* 1.3 81.8 - - - +
54F MET* 1.3 60.8 + - - +
55F ARG* 4.8 2.2 - - - +
111F ILE 4.6 1.8 - - - +
112F HIS* 3.1 33.5 + - + +
117F HIS* 3.3 16.4 + - + +
----------------------------------------------------------
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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