Contacts of the helix formed by residues 46 - 76 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 1.3 82.3 - - + +
47F PHE* 1.3 65.8 + - - +
48F ILE 3.7 1.1 - - - -
49F GLY* 3.6 11.4 + - - +
50F VAL* 3.8 9.4 + - - +
102F VAL* 3.6 31.8 - - - +
103F GLN* 4.8 4.3 + - - +
155F HIS* 4.4 3.8 - - - -
45G PRO* 2.6 37.7 + - - +
46G ASN* 4.2 13.2 - - + +
46K ASN* 4.1 19.7 - - + +
155K HIS* 4.7 0.9 - - - -
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Residues in contact with PHE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F HIS 5.0 1.1 - - - -
42F VAL* 3.4 37.7 - - + -
44F GLY 3.6 19.6 + - - +
45F PRO 3.2 4.4 + - - -
46F ASN* 1.3 77.4 - - - +
48F ILE* 1.3 74.1 + - + +
49F GLY 3.1 0.2 + - - -
50F VAL* 3.1 4.2 + - - +
51F HIS* 3.1 54.0 + + + -
102F VAL* 4.7 7.2 - - - -
150K TRP* 4.2 12.3 - + - -
151K PHE* 3.4 32.8 - + - -
154K ALA* 3.7 24.5 - - + +
155K HIS* 3.2 32.5 + + + +
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Residues in contact with ILE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ASN 3.7 0.2 - - - -
47F PHE* 1.3 82.2 - - + +
49F GLY* 1.3 72.0 + - - +
50F VAL 3.1 0.3 + - - -
51F HIS* 4.1 8.5 - - + -
52F GLU* 3.0 49.1 + - + +
49K GLY* 4.0 25.1 - - - +
53K MET* 3.2 43.3 - - + -
151K PHE* 4.1 26.9 - - + -
155K HIS* 3.5 13.9 + - + +
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Residues in contact with GLY 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ASN* 3.6 8.8 + - - +
47F PHE 3.1 1.8 + - - -
48F ILE* 1.3 85.4 - - - +
50F VAL* 1.3 60.2 + - - +
52F GLU* 4.0 2.3 - - - +
53F MET* 3.1 20.8 + - - +
155F HIS* 5.6 0.7 - - - -
48G ILE* 4.1 22.6 - - - +
49G GLY* 5.2 5.6 - - - -
49K GLY* 5.2 6.0 - - - -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 5.4 0.7 - - + -
42F VAL* 4.6 13.5 - - + -
46F ASN* 3.8 6.2 + - - +
47F PHE 3.1 6.0 + - - +
49F GLY* 1.3 71.1 - - - +
51F HIS* 1.3 62.6 + - - +
53F MET* 2.6 39.9 + - + +
54F ILE* 3.1 30.0 + - + +
102F VAL* 3.2 34.8 - - + -
105F HIS* 6.5 0.2 - - + -
106F LEU* 4.0 20.9 - - + -
155F HIS* 4.0 16.8 - - + +
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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
----------------------------------------------------------
39F HIS* 2.7 80.9 + + - +
42F VAL* 5.4 2.8 - - - +
47F PHE* 3.1 32.6 + + + +
48F ILE* 3.5 15.3 - - + +
50F VAL* 1.3 81.0 - - - +
52F GLU* 1.3 69.1 + - + +
54F ILE* 3.6 11.6 + - - +
55F ASP 4.1 0.5 + - - -
150K TRP* 4.3 12.6 - + - -
151K PHE* 3.7 26.8 - + - -
70L GLU* 3.3 20.7 + - + -
206L FE 4.1 0.4 - - - -
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F HIS* 5.1 2.2 - - - -
48F ILE* 3.0 39.1 + - + +
49F GLY 4.1 2.0 - - - +
51F HIS* 1.3 80.8 - - + +
53F MET* 1.3 64.4 + - - +
54F ILE 3.1 3.9 + - - -
55F ASP* 3.5 8.9 + - + +
56F PRO* 3.3 18.2 - - - +
53K MET* 6.1 1.4 - - - -
151K PHE* 6.2 0.5 - - - -
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Residues in contact with MET 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLY 3.1 16.6 + - - +
50F VAL* 2.6 30.9 + - + +
52F GLU* 1.3 71.4 - - - +
54F ILE* 1.3 60.9 + - + +
56F PRO* 3.7 11.0 - - - +
57F GLN* 4.5 1.9 + - - +
106F LEU* 4.1 26.5 - - + -
148F PHE* 4.0 29.1 - - + -
151F PHE* 4.0 21.1 - - + -
152F VAL* 4.7 2.5 - - - -
155F HIS* 3.8 15.7 - - + +
48G ILE* 3.3 38.8 - - + -
52G GLU* 6.0 1.1 - - - -
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 3.6 31.0 - - + +
38F VAL* 3.1 34.1 - - + +
39F HIS* 3.9 17.5 - - + -
42F VAL* 4.9 0.2 - - + -
50F VAL* 3.4 30.1 - - + +
51F HIS* 3.8 7.2 - - - +
52F GLU 3.1 1.2 - - - -
53F MET* 1.3 83.4 - - + +
55F ASP* 1.3 70.2 + - - +
56F PRO 3.2 2.0 - - - -
57F GLN* 3.0 14.2 + - - +
58F VAL* 3.1 26.3 + - + +
106F LEU* 6.1 0.9 - - + -
109F LEU* 5.5 3.1 - - + -
148F PHE* 4.7 8.1 - - + -
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Residues in contact with ASP 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LYS* 3.1 29.9 + - - +
39F HIS* 3.2 25.8 + - - -
51F HIS 4.1 2.3 + - - +
52F GLU* 3.5 11.3 + - + +
54F ILE* 1.3 76.1 - - - +
56F PRO* 1.3 61.1 - - + +
58F VAL* 2.8 10.6 + - - +
59F GLU* 2.7 42.1 + - + +
206L FE 3.9 4.5 - - - -
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Residues in contact with PRO 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU 3.3 14.6 - - - +
53F MET* 3.7 8.1 - - - +
54F ILE 3.4 3.6 - - - -
55F ASP* 1.3 93.5 - - + +
57F GLN* 1.3 56.0 + - - +
59F GLU* 3.2 7.8 + - + +
60F LEU* 2.8 34.7 + - - +
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 4.6 5.2 - - + -
53F MET 4.5 0.8 + - - +
54F ILE* 3.0 7.9 + - - +
56F PRO* 1.3 78.5 - - - +
58F VAL* 1.3 56.3 + - - +
60F LEU* 3.6 20.1 - - - +
61F VAL* 2.9 43.4 + - + +
64F TYR* 5.6 1.4 - - - -
113F TYR* 3.1 28.4 + - - +
144F GLU* 4.2 4.8 + - - +
145F LEU* 3.6 26.7 - - - +
148F PHE* 3.0 58.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 4.1 7.3 - - + +
35F LEU* 3.3 31.6 - - + -
36F LYS* 3.6 25.1 - - + +
39F HIS* 5.7 0.2 - - + -
54F ILE* 3.2 23.8 - - + +
55F ASP* 2.8 12.2 + - - +
57F GLN* 1.3 75.5 - - - +
59F GLU* 1.3 57.1 + - + +
60F LEU 2.7 14.4 + - - -
61F VAL* 3.0 4.3 + - - +
62F ARG* 2.9 24.1 + - - +
62L ARG* 2.8 38.3 + - - +
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ASP* 2.7 24.1 + - + +
56F PRO* 3.9 7.6 - - + +
58F VAL* 1.3 72.5 - - + +
60F LEU* 1.3 57.8 + - - +
62F ARG* 4.4 4.4 - - - +
63F GLY* 3.6 13.9 + - - -
59L GLU* 3.8 28.2 - - - +
62L ARG* 3.8 20.2 + - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F PRO 2.8 17.5 + - - +
57F GLN* 3.6 19.3 - - - +
58F VAL 2.7 1.4 + - - -
59F GLU* 1.3 77.4 - - - +
61F VAL* 1.3 59.5 - - - +
62F ARG 3.2 1.1 - - - -
63F GLY* 2.8 18.6 + - - -
64F TYR* 2.9 45.6 + - + +
144F GLU* 3.5 33.7 - - + +
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 3.7 29.9 - - + +
31F LEU* 3.6 30.7 - - + -
32F HIS* 3.5 25.8 - - + -
35F LEU* 5.1 1.6 - - + -
57F GLN* 2.9 38.4 + - + +
58F VAL* 3.0 2.3 + - - +
60F LEU* 1.3 70.7 - - - +
62F ARG* 1.3 58.5 + - - +
63F GLY 2.9 4.7 - - - -
64F TYR* 2.8 27.5 + - + +
65F ALA* 3.1 10.6 + - - +
113F TYR* 4.4 1.8 - - - +
145F LEU* 4.5 4.7 - - + -
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 4.2 17.5 - - + +
58F VAL 2.9 9.4 + - - +
59F GLU* 4.5 5.8 - - - +
61F VAL* 1.3 77.5 - - - +
63F GLY* 1.3 60.8 + - - +
65F ALA* 3.2 22.2 + - + +
66F ASP* 3.5 8.8 + - - +
32L HIS* 3.3 29.2 + - - -
36L LYS* 4.6 18.8 - - + +
58L VAL* 2.8 38.2 + - - +
59L GLU* 3.8 23.2 + - - +
62L ARG* 3.3 65.3 - - - +
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLU 3.6 9.1 + - - -
60F LEU* 2.8 15.5 + - - -
62F ARG* 1.3 81.4 - - - +
64F TYR* 1.3 63.2 + - - +
66F ASP* 3.9 4.5 + - - +
67F GLU* 3.4 23.8 + - - +
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Residues in contact with TYR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 3.6 13.0 - + + -
57F GLN* 5.6 0.7 - - - -
60F LEU* 2.9 46.9 + - + +
61F VAL* 2.8 19.7 + - + +
63F GLY* 1.3 76.2 - - - +
65F ALA* 1.3 58.6 + - - +
67F GLU* 3.4 12.9 - - - +
68F VAL* 2.9 35.7 + - - +
140F ALA* 4.5 2.8 + - + -
141F HIS* 3.1 55.7 - + + +
144F GLU* 3.3 26.6 + - + +
145F LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 4.4 6.0 - - + +
28F TYR* 4.2 13.2 - - + -
29F ASN* 4.3 19.3 - - - +
32F HIS* 5.1 1.6 - - + +
61F VAL 3.1 9.2 + - - +
62F ARG* 3.3 19.5 - - + +
63F GLY 3.2 0.4 - - - -
64F TYR* 1.3 74.6 - - - +
66F ASP* 1.3 68.0 + - - +
67F GLU 3.0 1.6 + - - -
68F VAL* 3.1 3.7 + - - +
69F ALA* 2.9 25.5 + - - +
36L LYS* 6.2 0.9 - - + -
40L TRP* 4.1 13.2 - - + -
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Residues in contact with ASP 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG 3.5 7.7 + - - +
63F GLY* 4.3 6.7 - - - +
65F ALA* 1.3 77.2 - - - +
67F GLU* 1.3 57.7 + - - +
70F GLU* 2.8 55.0 + - - +
212F FE 2.5 31.8 - - - -
36L LYS* 3.0 27.0 + - - +
39L HIS* 3.0 8.1 + - - -
40L TRP* 3.2 13.0 + - - +
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 5.1 8.0 + - - +
63F GLY 3.4 16.0 + - - +
64F TYR* 3.4 16.9 - - - +
65F ALA 3.0 0.2 - - - -
66F ASP* 1.3 83.0 - - - +
68F VAL* 1.3 62.6 + - - +
70F GLU* 4.0 4.6 - - - +
71F ARG* 3.2 18.9 + - - +
137F LEU* 4.7 17.5 - - + +
141F HIS* 3.0 28.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.6 43.1 - - + +
24F GLN* 4.8 4.9 - - + -
25F LEU* 4.3 14.8 - - + +
28F TYR* 3.7 21.3 - - + -
64F TYR 2.9 19.6 + - - +
65F ALA* 3.8 2.2 - - - +
67F GLU* 1.3 71.3 - - - +
69F ALA* 1.3 62.1 + - - +
71F ARG* 2.8 29.1 + - - +
72F ILE* 2.9 8.3 + - + +
137F LEU* 4.4 10.5 - - + -
138F LEU* 4.9 2.7 - - + -
141F HIS* 3.9 12.1 - - + -
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 3.2 26.8 - - + +
65F ALA 2.9 12.2 + - - +
68F VAL* 1.3 68.9 - - - +
70F GLU* 1.3 54.7 + - - +
71F ARG 2.7 6.0 + - - -
72F ILE* 2.7 27.5 + - - +
73F ALA* 3.0 9.9 + - - +
79F PRO* 3.4 13.9 - - + +
40L TRP* 3.2 40.2 - - + +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 2.8 44.6 + - - +
150E TRP* 4.3 24.0 - - + -
151E PHE* 5.0 1.0 - - - -
66F ASP* 2.8 44.2 + - - +
67F GLU* 4.0 1.3 - - - +
69F ALA* 1.3 73.0 - - - +
71F ARG* 1.3 50.2 + - - +
73F ALA* 4.2 4.4 - - - +
74F THR* 2.5 31.5 + - - -
212F FE 2.1 28.5 - - - -
40L TRP* 3.7 13.7 - - + -
51L HIS* 3.2 23.1 + - - -
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 3.9 2.0 - - - +
143E GLY* 4.3 9.1 + - - -
146E GLU* 2.9 40.1 + - - +
147E LYS* 5.8 0.8 - - - +
6F ILE* 5.3 0.7 - - - -
21F LEU* 3.8 19.5 - - + -
67F GLU 3.2 13.9 + - - +
68F VAL* 2.8 17.3 + - - +
69F ALA 2.7 1.0 + - - -
70F GLU* 1.3 77.4 - - - +
72F ILE* 1.3 63.7 + - - +
74F THR* 3.2 15.2 + - - +
75F LEU* 3.2 32.6 + - + +
131F ASP* 2.8 29.3 + - - -
133F VAL* 3.4 24.1 - - - +
134F SER* 3.0 14.5 + - - +
137F LEU* 4.7 17.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ALA* 4.5 9.9 - - + +
21F LEU* 3.7 22.7 - - + -
22F GLN* 3.5 44.4 - - + +
25F LEU* 4.5 4.0 - - + -
68F VAL* 2.9 16.6 + - + +
69F ALA* 2.7 22.3 + - - +
71F ARG* 1.3 72.0 - - - +
73F ALA* 1.3 58.5 + - - +
75F LEU* 2.8 31.8 + - - +
76F GLY 3.2 5.0 + - - -
77F LYS* 3.7 21.3 + - + +
78F SER 4.4 0.9 - - - -
79F PRO* 3.5 24.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 3.6 37.4 + - + +
4F PHE* 3.9 1.6 - - - -
69F ALA 3.0 8.6 + - - +
70F GLU* 4.2 2.5 - - - +
72F ILE* 1.3 79.1 - - - +
74F THR* 1.3 64.2 + - - +
76F GLY* 3.1 10.7 + - - -
77F LYS 3.5 12.8 - - - +
79F PRO* 3.7 15.9 - - + +
40L TRP* 4.3 7.4 - - + +
99L ARG* 3.7 16.3 + - - +
----------------------------------------------------------
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Residues in contact with THR 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E GLU* 3.5 35.4 - - + +
147E LYS* 4.2 9.0 - - - +
149E GLN* 5.8 1.3 - - - +
150E TRP* 3.8 25.3 - - + +
153E ARG* 5.1 1.6 + - - -
4F PHE* 3.4 15.2 - - - -
6F ILE* 3.2 19.7 - - + +
70F GLU 2.5 23.8 + - - -
71F ARG* 3.2 19.8 + - - +
72F ILE 3.1 0.2 - - - -
73F ALA* 1.3 80.5 - - - +
75F LEU* 1.3 61.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F PHE* 3.8 1.4 - - - +
5F THR* 3.5 26.7 + - - -
6F ILE* 3.4 22.7 - - + -
9F LEU* 3.9 24.0 - - + -
14F ALA* 3.8 24.7 - - + +
17F VAL* 3.8 28.3 - - + -
18F ALA* 3.9 14.8 - - + +
21F LEU* 4.5 8.7 - - + -
71F ARG* 3.2 25.5 + - - +
72F ILE* 2.8 12.7 + - - +
74F THR* 1.3 81.0 - - - +
76F GLY* 1.3 55.7 + - - +
77F LYS 3.8 2.0 - - - +
131F ASP* 5.3 0.2 - - - +
134F SER* 4.8 2.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F PHE* 4.1 22.2 - - - -
72F ILE 3.2 0.2 + - - -
73F ALA 3.1 11.5 + - - -
75F LEU* 1.3 80.5 - - - +
77F LYS* 1.3 63.4 + - - +
99L ARG* 3.1 27.8 + - - -
----------------------------------------------------------
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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