Contacts of the helix formed by residues 46 - 76 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASN* 4.2 18.8 - - + +
155C HIS* 4.8 1.1 - - - -
45H PRO* 2.7 37.3 + - - +
46H ASN* 4.2 12.1 - - + +
45J PRO* 1.3 82.7 - - + +
47J PHE* 1.3 65.5 + - - +
48J ILE 3.7 1.1 - - - -
49J GLY* 3.6 10.7 + - - +
50J VAL* 3.8 9.1 + - - +
102J VAL* 3.6 32.0 - - - +
103J GLN* 4.8 4.9 + - - +
155J HIS* 4.4 3.6 - - - -
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Residues in contact with PHE 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C TRP* 4.2 12.6 - + - -
151C PHE* 3.3 33.4 - + - -
154C ALA* 3.8 26.0 - - + +
155C HIS* 3.2 34.7 + + + +
39J HIS 5.0 1.3 - - - -
42J VAL* 3.5 37.0 - - + +
44J GLY 3.7 16.4 + - - +
45J PRO 3.2 3.8 + - - -
46J ASN* 1.3 77.4 - - - +
48J ILE* 1.3 73.4 + - + +
49J GLY 3.0 0.2 + - - -
50J VAL* 3.1 3.8 + - - +
51J HIS* 3.0 53.5 + + + -
102J VAL* 4.7 7.0 - - - -
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Residues in contact with ILE 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY* 4.0 24.7 - - - +
53C MET* 3.3 44.4 - - + -
151C PHE* 4.2 26.7 - - + -
155C HIS* 3.5 13.6 + - + +
46J ASN 3.7 0.2 - - - -
47J PHE* 1.3 83.5 - - + +
49J GLY* 1.3 73.6 + - - +
50J VAL 3.1 0.3 + - - -
51J HIS* 4.1 8.7 - - + -
52J GLU* 2.9 49.8 + - - +
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Residues in contact with GLY 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY* 5.2 6.4 - - - -
48H ILE* 4.1 23.0 - - - +
49H GLY* 5.3 4.9 - - - -
46J ASN* 3.6 9.8 + - - -
47J PHE 3.0 1.6 + - - -
48J ILE* 1.3 85.1 - - - +
50J VAL* 1.3 60.7 + - - +
52J GLU* 3.7 2.5 + - - +
53J MET* 3.1 21.1 + - - +
155J HIS* 5.5 0.4 - - - -
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Residues in contact with VAL 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 5.4 0.7 - - + -
42J VAL* 4.6 13.7 - - + -
46J ASN* 3.8 6.0 + - - +
47J PHE 3.1 6.5 + - - +
49J GLY* 1.3 70.1 - - - +
51J HIS* 1.3 71.6 + - - +
53J MET* 2.6 31.2 + - + +
54J ILE* 3.1 29.0 + - + +
102J VAL* 3.3 34.8 - - + -
105J HIS* 6.5 0.4 - - + -
106J LEU* 4.0 14.1 - - + -
155J HIS* 4.0 25.8 - - + +
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Residues in contact with HIS 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.3 22.9 + - + -
210A FE 4.0 1.0 - - - -
150C TRP* 4.5 7.6 - + - -
151C PHE* 3.7 26.1 - + - -
39J HIS* 2.7 78.3 + + - +
42J VAL* 5.4 3.1 - - + +
47J PHE* 3.0 38.6 + + + +
48J ILE* 3.5 14.8 - - + +
50J VAL* 1.3 80.6 - - - +
52J GLU* 1.3 68.2 + - + +
54J ILE* 3.6 11.6 + - - +
55J ASP 4.1 0.7 + - - -
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Residues in contact with GLU 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET* 6.0 1.6 - - - -
151C PHE* 6.2 0.2 - - - -
39J HIS* 5.2 1.8 - - - -
48J ILE* 2.9 41.4 + - + +
49J GLY 4.1 2.5 - - - +
51J HIS* 1.3 81.7 - - + +
53J MET* 1.3 64.7 + - - +
54J ILE 3.1 4.0 + - - -
55J ASP* 3.6 8.3 + - + +
56J PRO* 3.3 19.1 - - - +
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Residues in contact with MET 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ILE* 3.3 38.4 - - + -
52H GLU* 6.1 0.7 - - - -
49J GLY 3.1 16.0 + - - +
50J VAL* 2.6 30.9 + - + +
52J GLU* 1.3 73.0 - - - +
54J ILE* 1.3 60.0 + - + +
56J PRO* 3.6 11.6 - - - +
57J GLN* 4.5 2.3 + - - +
106J LEU* 4.1 26.9 - - + -
148J PHE* 4.1 29.2 - - + -
151J PHE* 4.0 21.3 - - + -
152J VAL* 4.7 2.2 - - - -
155J HIS* 3.8 17.0 - - + +
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Residues in contact with ILE 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 3.5 37.2 - - + +
38J VAL* 3.1 33.9 - - + -
39J HIS* 3.9 16.8 - - + -
42J VAL* 4.9 0.4 - - + -
50J VAL* 3.4 30.7 - - + +
51J HIS* 3.8 7.0 - - - +
52J GLU 3.1 0.8 - - - -
53J MET* 1.3 84.1 - - + +
55J ASP* 1.3 68.7 + - - +
56J PRO 3.3 0.4 - - - -
57J GLN* 3.0 14.0 + - - +
58J VAL* 3.1 20.7 + - + +
106J LEU* 6.2 0.9 - - + -
109J LEU* 5.5 2.9 - - + -
148J PHE* 4.7 8.1 - - + -
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Residues in contact with ASP 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A FE 4.0 4.0 - - - -
36J LYS* 3.1 29.1 + - - +
39J HIS* 3.2 26.8 + - - -
51J HIS 4.1 1.8 + - - +
52J GLU* 3.6 11.2 + - + +
54J ILE* 1.3 75.7 - - - +
56J PRO* 1.3 66.5 - - + +
58J VAL* 3.0 8.8 + - - +
59J GLU* 2.8 37.2 + - + +
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Residues in contact with PRO 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLU 3.3 14.8 - - - +
53J MET* 3.6 8.1 - - - +
54J ILE 3.5 3.4 - - - -
55J ASP* 1.3 94.1 - - + +
57J GLN* 1.3 56.3 + - - +
59J GLU* 3.3 6.9 + - + +
60J LEU* 2.9 34.1 + - - +
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Residues in contact with GLN 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 4.6 5.2 - - + -
53J MET 4.5 1.2 + - - +
54J ILE 3.0 7.5 + - - +
56J PRO* 1.3 79.8 - - - +
58J VAL* 1.3 57.4 + - - +
60J LEU* 3.5 19.0 - - - +
61J VAL* 3.0 43.7 + - + +
64J TYR* 5.6 1.0 - - - -
113J TYR* 3.1 29.1 + - - +
144J GLU* 4.2 5.4 + - - +
145J LEU* 3.6 26.9 - - - +
148J PHE* 3.0 58.4 - - + +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 2.7 38.7 + - - +
32J HIS* 4.2 7.1 - - + +
35J LEU* 3.4 30.7 - - + -
36J LYS* 3.6 24.9 - - + +
39J HIS* 5.7 0.2 - - + -
54J ILE* 3.2 24.2 - - + +
55J ASP* 3.0 11.2 + - - +
57J GLN* 1.3 73.5 - - - +
59J GLU* 1.3 55.6 + - + +
60J LEU 2.7 14.6 + - - -
61J VAL* 2.9 5.7 + - - +
62J ARG* 2.8 25.8 + - - +
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Residues in contact with GLU 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.8 28.7 - - - +
62A ARG* 3.7 21.2 + - - +
55J ASP* 2.8 23.8 + - + +
56J PRO* 3.7 7.0 - - + +
58J VAL* 1.3 73.3 - - + +
60J LEU* 1.3 59.4 + - - +
62J ARG* 4.2 5.2 - - - +
63J GLY* 3.5 13.9 + - - -
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Residues in contact with LEU 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J PRO 2.9 18.2 + - - +
57J GLN* 3.5 19.7 - - - +
58J VAL 2.7 1.2 - - - -
59J GLU* 1.3 79.1 - - - +
61J VAL* 1.3 60.9 + - - +
62J ARG 3.2 1.1 - - - -
63J GLY* 2.8 18.3 + - - -
64J TYR* 3.0 42.7 + - + +
144J GLU* 3.5 33.2 - - + +
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Residues in contact with VAL 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 3.7 28.6 - - + +
31J LEU* 3.6 31.4 - - + -
32J HIS* 3.5 27.1 - - + -
35J LEU* 5.1 1.1 - - + -
57J GLN* 3.0 41.7 + - + +
58J VAL* 2.9 2.7 + - - +
60J LEU* 1.3 70.8 - - - +
62J ARG* 1.3 67.7 + - - +
63J GLY 2.9 1.8 - - - -
64J TYR* 2.8 23.5 + - + +
65J ALA* 3.1 10.2 + - - +
113J TYR* 4.4 1.8 - - - +
145J LEU* 4.6 4.7 - - + -
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Residues in contact with ARG 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 3.4 28.7 + - - -
36A LYS* 4.5 19.1 - - + +
58A VAL* 2.7 37.5 + - - +
59A GLU* 3.8 23.0 + - - +
62A ARG* 3.4 58.1 - - - +
32J HIS* 4.2 18.9 + - + +
58J VAL 2.8 14.6 + - - +
59J GLU* 4.5 6.3 - - - +
61J VAL* 1.3 78.9 - - - +
63J GLY* 1.3 61.8 + - - +
65J ALA* 3.1 21.6 + - + +
66J ASP* 3.4 8.5 + - - +
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Residues in contact with GLY 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J GLU 3.5 9.1 + - - -
60J LEU* 2.8 15.8 + - - -
62J ARG* 1.3 82.3 - - - +
64J TYR* 1.3 61.6 + - - +
66J ASP* 3.8 5.1 + - - +
67J GLU* 3.3 23.6 + - - +
----------------------------------------------------------
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Residues in contact with TYR 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 3.6 14.8 - + + -
57J GLN* 5.6 1.1 - - - -
60J LEU* 3.0 47.0 + - + +
61J VAL* 2.8 19.1 + - + +
63J GLY* 1.3 76.0 - - - +
65J ALA* 1.3 60.2 + - - +
67J GLU* 3.4 14.0 - - - +
68J VAL* 3.0 35.3 + - - +
140J ALA* 4.6 3.0 + - + -
141J HIS* 3.2 51.8 - + + -
144J GLU* 3.4 26.3 + - + +
145J LEU* 4.1 23.1 - - + -
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Residues in contact with ALA 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 6.2 0.7 - - + -
40A TRP* 4.1 13.9 - - + -
25J LEU* 4.3 5.1 - - + +
28J TYR* 4.4 13.5 - - + -
29J ASN* 4.2 19.1 - - - +
32J HIS* 5.1 1.8 - - + -
61J VAL 3.1 7.5 + - - +
62J ARG* 3.1 21.3 + - + +
64J TYR* 1.3 74.1 - - - +
66J ASP* 1.3 68.0 + - - +
67J GLU 3.0 1.2 + - - -
68J VAL* 3.1 3.2 + - - +
69J ALA* 2.9 25.8 + - - +
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Residues in contact with ASP 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 3.1 20.3 + - - +
39A HIS* 3.1 10.9 + - - -
40A TRP* 3.2 17.7 + - - +
62J ARG 3.4 7.7 + - - +
63J GLY* 4.3 6.3 - - - +
65J ALA* 1.3 76.7 - - - +
67J GLU* 1.3 57.4 + - - +
70J GLU* 2.7 56.5 + - - +
201J FE 2.5 29.9 - - - -
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Residues in contact with GLU 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLY 3.3 14.8 + - - +
64J TYR* 3.4 18.0 - - - +
65J ALA 3.0 0.8 - - - -
66J ASP* 1.3 81.4 - - - +
68J VAL* 1.3 62.6 + - - +
70J GLU* 4.0 5.0 - - - +
71J ARG* 3.2 20.6 + - - +
137J LEU* 4.7 17.7 - - + +
141J HIS* 3.0 28.5 + - + +
147L LYS* 5.0 8.0 + - - +
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 3.6 43.5 - - + +
24J GLN* 4.8 2.0 - - + -
25J LEU* 4.3 13.7 - - + +
28J TYR* 3.6 21.8 - - + -
64J TYR 3.0 19.3 + - - +
65J ALA* 3.8 2.2 - - - +
67J GLU* 1.3 72.1 - - - +
69J ALA* 1.3 63.0 + - - +
71J ARG* 2.8 28.5 + - - +
72J ILE* 2.9 9.0 + - + +
137J LEU* 4.4 9.6 - - + -
138J LEU* 4.9 6.5 - - + -
141J HIS* 3.9 12.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.3 37.9 - - + +
25J LEU* 3.2 28.2 - - + +
65J ALA 2.9 12.2 + - - +
68J VAL* 1.3 69.2 - - - +
70J GLU* 1.3 53.8 + - - +
71J ARG 2.7 14.8 + - - -
72J ILE* 2.7 17.5 + - - +
73J ALA* 3.1 10.4 + - - +
79J PRO* 3.4 14.6 - - + +
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Residues in contact with GLU 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.7 13.2 - - + -
51A HIS* 3.3 21.0 + - - -
66J ASP* 2.7 47.3 + - - +
67J GLU* 4.1 0.8 - - - +
69J ALA* 1.3 71.7 - - - +
71J ARG* 1.3 50.5 + - - +
73J ALA* 4.2 4.0 - - - +
74J THR* 2.5 32.2 + - - -
201J FE 2.1 28.7 - - - -
147L LYS* 2.7 45.0 + - - +
150L TRP* 4.3 24.3 - - + -
151L PHE* 5.0 1.4 - - - -
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Residues in contact with ARG 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 5.3 0.7 - - - -
21J LEU* 3.8 19.7 - - + -
67J GLU 3.2 13.9 + - - +
68J VAL* 2.8 17.3 + - - +
69J ALA 2.7 0.6 + - - -
70J GLU* 1.3 77.5 - - - +
72J ILE* 1.3 63.3 + - - +
74J THR* 3.1 26.6 + - - +
75J LEU* 3.1 22.2 + - + +
131J ASP* 2.8 26.7 + - - -
133J VAL* 3.4 24.8 - - - +
134J SER* 3.0 14.3 + - - +
137J LEU* 4.7 17.0 - - + -
121L ARG* 3.7 4.0 - - - +
143L GLY* 4.3 9.7 + - - -
146L GLU* 2.9 40.1 + - - +
147L LYS* 5.2 1.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ALA* 4.5 10.5 - - + +
21J LEU* 3.7 21.5 - - + -
22J GLN* 3.5 44.2 - - + +
25J LEU* 4.4 5.4 - - + -
68J VAL* 2.9 19.3 + - + +
69J ALA* 2.7 20.6 + - - +
71J ARG* 1.3 72.0 - - - +
73J ALA* 1.3 58.6 + - - +
75J LEU* 2.8 32.5 + - - +
76J GLY 3.2 4.9 + - - -
77J LYS* 3.6 21.3 + - + +
78J SER 4.5 0.7 - - - -
79J PRO* 3.5 23.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.4 6.5 - - + +
99A ARG* 3.6 16.6 + - - +
4J PHE* 4.0 1.7 - - - -
69J ALA 3.1 8.8 + - - +
70J GLU* 4.2 2.9 - - - +
72J ILE* 1.3 78.3 - - - +
74J THR* 1.3 61.7 + - - +
76J GLY* 3.1 11.1 + - - -
77J LYS 3.5 12.6 - - - +
79J PRO* 3.7 15.0 - - + +
150L TRP* 3.5 39.2 + - + +
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Residues in contact with THR 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 3.5 14.2 - - - -
6J ILE* 3.2 20.3 - - + +
70J GLU 2.5 23.6 + - - -
71J ARG* 3.1 18.4 + - - +
72J ILE 3.1 0.4 - - - -
73J ALA* 1.3 80.6 - - - +
75J LEU* 1.3 61.4 + - - +
146L GLU* 3.4 36.1 - - + +
147L LYS* 4.2 8.1 - - - +
149L GLN* 5.7 1.6 - - - +
150L TRP* 3.7 26.4 - - + +
153L ARG* 5.0 1.7 + - - -
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Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 3.9 1.1 - - - +
5J THR* 3.5 28.1 + - - -
6J ILE* 3.3 22.4 - - + -
9J LEU* 3.9 23.6 - - + -
14J ALA* 3.8 25.5 - - + +
17J VAL* 3.7 29.8 - - + -
18J ALA* 3.9 14.1 - - + +
21J LEU* 4.5 8.5 - - + -
71J ARG* 3.1 25.6 + - - +
72J ILE* 2.8 13.2 + - - +
74J THR* 1.3 80.6 - - - +
76J GLY* 1.3 55.4 + - - +
77J LYS 3.8 2.9 - - - +
131J ASP* 5.4 0.2 - - - +
134J SER* 4.8 3.1 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.1 24.1 + - - -
4J PHE* 4.1 21.8 - - - -
72J ILE 3.2 0.8 + - - -
73J ALA 3.1 11.7 + - - -
74J THR 3.3 0.2 - - - -
75J LEU* 1.3 79.5 - - - +
77J LYS* 1.3 65.9 + - - +
----------------------------------------------------------
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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