Contacts of the helix formed by residues 48 - 76 (chain J) in PDB entry 5JKL
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 LEU 48 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H ASN* 3.9 14.6 - - - +
157H LYS* 6.6 0.2 - - + -
41J PHE* 2.9 35.8 + - + +
46J VAL* 3.7 13.2 - - + +
47J ALA* 1.3 82.6 - - - +
49J LYS* 1.3 64.5 + - - +
50J ASN 3.3 2.5 - - - -
51J PHE* 3.3 23.0 + - + -
52J ALA* 3.1 17.3 + - - +
167J GLU* 4.2 24.2 - - + +
168J TYR* 4.1 16.4 - - + +
171J ASP* 3.3 27.1 - - + +
172J LYS* 4.8 2.7 - - - +
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Residues in contact with LYS 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H GLU* 5.7 2.8 + - - -
150H ASP* 4.3 19.7 - - + +
41J PHE 4.9 1.1 - - - +
42J ASP* 5.9 5.4 - - - +
47J ALA* 3.7 8.8 + - - +
48J LEU* 1.3 72.4 - - - +
50J ASN* 1.3 64.9 + - - +
52J ALA* 3.4 9.3 + - - +
53J LYS* 2.9 35.8 + - - +
171J ASP* 3.5 3.6 + - - +
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Residues in contact with ASN 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LYS* 1.3 77.9 - - - +
51J PHE* 1.3 60.9 + - - +
53J LYS* 3.8 20.9 + - - +
54J TYR* 2.9 30.0 + - - +
171J ASP* 2.9 51.7 + - - +
172J LYS* 4.3 10.3 - - - +
175J LEU* 3.8 19.0 - - + +
176J GLY* 3.7 18.5 - - - -
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Residues in contact with PHE 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J PHE* 3.6 19.3 - + + -
48J LEU* 3.3 21.3 + - + +
50J ASN* 1.3 75.3 - - - +
52J ALA* 1.3 64.0 + - - +
54J TYR* 3.6 1.4 - - - +
55J PHE* 3.0 42.9 + + - -
96J GLY* 3.4 38.1 - - - -
100J MET* 3.8 22.4 - - + -
155J LEU* 4.2 10.1 - - + -
167J GLU* 3.7 23.6 - - + -
170J PHE* 3.6 25.1 - + - -
171J ASP* 3.0 28.0 + - + -
175J LEU* 3.7 14.3 - - + +
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Residues in contact with ALA 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J SER* 2.7 48.2 + - - +
41J PHE* 3.7 6.0 - - + +
42J ASP* 4.2 15.5 - - + +
48J LEU 3.1 13.6 + - - +
49J LYS* 3.4 12.6 - - - +
50J ASN 3.2 0.2 - - - -
51J PHE* 1.3 78.0 - - - +
53J LYS* 1.3 62.0 + - + +
55J PHE 3.4 0.2 + - - -
56J LEU* 3.0 11.5 + - - +
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Residues in contact with LYS 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LYS* 2.9 25.0 + - - +
50J ASN* 3.8 20.7 + - - +
51J PHE 3.3 0.2 - - - -
52J ALA* 1.3 78.4 - - + +
54J TYR* 1.3 61.2 + - - +
56J LEU* 3.3 7.9 + - + +
57J HIS* 3.0 25.6 + - - +
175J LEU 5.9 1.1 - - - +
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Residues in contact with TYR 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 5.7 0.2 - + - -
50J ASN 2.9 18.9 + - - +
51J PHE 3.6 3.8 - - - +
53J LYS* 1.3 76.2 - - - +
55J PHE* 1.3 95.2 + + - +
57J HIS* 3.4 8.2 + + - +
58J GLN* 3.1 49.5 + - + +
100J MET* 3.9 18.8 - - + -
147J GLU* 2.7 32.0 + - - +
148J LEU* 3.8 15.3 - - + +
151J HIS* 3.7 21.6 - + - -
175J LEU* 3.9 22.4 - - + +
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Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.5 49.2 - + - +
37J MET* 3.9 18.2 - - + -
38J SER* 3.8 8.3 - - - +
41J PHE* 3.5 35.2 - + - -
51J PHE* 3.0 35.9 + + - +
54J TYR* 1.3 96.7 - + - +
56J LEU* 1.3 65.7 + - - +
58J GLN* 3.3 2.1 + - - -
59J SER* 3.0 22.7 + - - -
99J ALA* 3.9 18.8 - - + -
100J MET* 3.8 25.4 - - + -
103J ALA* 4.3 6.1 - - + -
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Residues in contact with LEU 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 3.8 29.4 - - + -
38J SER* 3.5 16.7 - - - +
39J TYR* 4.1 22.0 - - + +
52J ALA 3.0 11.7 + - - +
53J LYS* 3.8 7.9 - - + +
54J TYR 3.3 0.2 - - - -
55J PHE* 1.3 77.5 - - - +
57J HIS* 1.3 61.4 + - - +
59J SER* 3.2 6.3 + - - -
60J HIS* 3.0 52.2 + - + +
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Residues in contact with HIS 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J LYS 3.0 17.4 + - - +
54J TYR* 3.5 6.5 - + - +
56J LEU* 1.3 77.2 - - - +
58J GLN* 1.3 84.7 + - - +
60J HIS* 3.2 9.4 + - - +
61J GLU* 3.0 48.1 + - + +
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Residues in contact with GLN 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.7 33.8 + - + -
54J TYR* 3.1 56.6 + - + +
55J PHE* 3.6 7.9 - - - +
56J LEU 3.2 0.2 - - - -
57J HIS* 1.3 92.3 + - - +
59J SER* 1.3 58.8 + - - +
61J GLU* 2.8 28.2 + - - +
62J GLU* 3.0 35.9 + - - +
107J GLU* 5.7 0.3 - - - +
144J ALA* 5.9 3.5 - - - +
147J GLU* 4.1 6.3 + - - -
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Residues in contact with SER 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER* 2.7 52.2 + - - +
34J TYR* 3.7 7.6 - - - +
35J LEU* 3.7 23.0 - - - +
55J PHE 3.0 12.9 + - - -
56J LEU* 3.2 13.9 + - - -
58J GLN* 1.3 76.3 - - - +
60J HIS* 1.3 70.7 + - - +
62J GLU 3.3 1.2 + - - -
63J ARG* 3.1 11.4 + - - +
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Residues in contact with HIS 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 6.0 0.2 - - - +
56J LEU* 3.0 45.3 + - + +
57J HIS* 3.8 8.0 - - - +
59J SER* 1.3 86.3 - - - +
61J GLU* 1.3 60.3 + - - +
63J ARG* 3.3 9.2 + - + +
64J GLU* 3.1 26.6 + - - +
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Residues in contact with GLU 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J HIS* 3.0 42.6 + - + +
58J GLN* 2.8 33.8 + - - +
60J HIS* 1.3 76.6 - - - +
62J GLU* 1.3 58.9 - - + +
64J GLU* 3.1 10.2 + - - +
65J HIS* 2.9 46.5 + - + +
140J GLU* 5.0 7.1 - - - +
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Residues in contact with GLU 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLU* 2.7 16.6 - - - +
30J ALA* 3.9 12.9 - - + +
31J SER* 3.6 30.3 - - - +
34J TYR* 3.8 17.7 - - + -
58J GLN* 3.0 22.0 + - - +
59J SER 3.7 0.2 - - - +
61J GLU* 1.3 74.6 - - - +
63J ARG* 1.3 67.2 + - - +
65J HIS* 3.1 14.7 + - - +
66J ALA* 3.0 22.7 + - - +
107J GLU* 3.2 24.2 - - - +
110J VAL* 6.2 0.4 - - - -
201J FE 2.0 31.9 - - - -
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Residues in contact with ARG 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J LEU* 4.0 23.4 - - - +
31J SER* 3.8 12.1 + - - +
59J SER 3.1 14.3 + - - +
60J HIS* 3.6 13.2 - - + +
61J GLU 3.3 0.2 - - - -
62J GLU* 1.3 77.2 - - - +
64J GLU* 1.3 62.3 + - - +
66J ALA* 3.3 4.7 + - - +
67J GLU* 3.0 64.7 + - - +
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Residues in contact with GLU 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J HIS* 3.1 14.6 + - + +
61J GLU* 3.1 10.5 + - - +
63J ARG* 1.3 80.7 - - - +
65J HIS* 1.3 63.6 - - + +
67J GLU* 2.7 34.2 + - - +
68J LYS* 3.0 24.5 + - - +
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Residues in contact with HIS 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLU* 3.3 17.9 - - - +
61J GLU* 2.9 40.2 + - + +
62J GLU* 3.1 20.3 + - - +
64J GLU* 1.3 77.6 - - + +
66J ALA* 1.3 61.0 + - - +
68J LYS* 4.7 2.9 - - + -
69J LEU* 3.3 12.2 + - - +
136J HIS 5.6 2.7 - - - -
137J TYR* 2.7 40.0 + + + -
140J GLU* 5.0 21.6 + - + +
141J GLN* 4.7 8.5 + - - -
201J FE 2.1 28.7 - - - -
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Residues in contact with ALA 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 4.1 8.7 - - + +
27J GLU* 3.8 19.2 - - + +
28J LEU* 3.6 33.2 - - + +
62J GLU 3.0 12.2 + - - +
63J ARG* 3.5 8.5 - - - +
65J HIS* 1.3 71.3 - - - +
67J GLU* 1.3 66.6 + - + +
69J LEU* 3.3 7.7 + - - +
70J MET* 3.0 30.1 + - - +
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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 ARG* 3.0 55.7 + - - +
64J GLU* 2.7 37.5 + - - +
66J ALA* 1.3 75.2 - - - +
68J LYS* 1.3 56.6 + - - +
70J MET* 3.3 17.2 + - - +
71J LYS* 2.9 27.2 + - - +
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Residues in contact with LYS 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J GLU 3.0 14.7 + - - +
65J HIS* 4.7 2.0 - - + -
66J ALA 3.3 0.4 - - - -
67J GLU* 1.3 75.6 - - - +
69J LEU* 1.3 57.2 + - - +
71J LYS* 3.4 14.9 + - + +
72J LEU* 2.9 26.3 + - - +
132J PHE* 3.9 12.9 - - + -
136J HIS* 3.1 49.1 + - + +
137J TYR* 3.4 19.1 - - + +
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Residues in contact with LEU 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ILE* 3.8 31.3 - - + +
23J GLN* 3.7 27.8 - - + -
24J ILE* 3.6 15.0 - - + +
27J GLU* 3.6 26.7 - - + -
65J HIS 3.3 11.6 + - - +
66J ALA* 3.3 8.4 + - - +
68J LYS* 1.3 75.6 - - - +
70J MET* 1.3 59.7 + - - +
72J LEU* 3.3 5.9 + - + +
73J GLN* 3.0 28.1 + - - +
114J LEU* 5.8 1.3 - - + -
117J LEU* 5.2 1.6 - - + -
132J PHE* 3.7 22.2 - - + -
133J ILE* 6.3 0.4 - - + -
137J TYR* 3.3 18.2 - - + +
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Residues in contact with MET 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 3.8 29.4 - - + -
28J LEU* 5.6 4.7 - - - -
66J ALA* 3.0 23.3 + - - +
67J GLU* 3.3 18.8 + - - +
69J LEU* 1.3 74.1 - - - +
71J LYS* 1.3 65.1 + - - +
73J GLN* 3.3 3.5 + - - +
74J ASN* 3.1 22.0 + - - +
80J ILE* 3.7 42.4 - - + +
82J LEU* 4.3 16.2 - - + -
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Residues in contact with LYS 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J GLU 2.9 14.0 + - - +
68J LYS* 3.5 17.5 - - + +
70J MET* 1.3 76.6 - - - +
72J LEU* 1.3 57.3 + - - +
74J ASN* 3.3 7.6 + - - +
75J GLN* 2.8 60.8 + - + +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 3.9 18.4 - - + +
20J ILE* 4.2 20.6 - - + -
68J LYS 2.9 14.9 + - - +
69J LEU* 3.4 8.7 - - - +
71J LYS* 1.3 73.8 - - - +
73J GLN* 1.3 67.8 + - - +
75J GLN* 3.0 16.8 + - - +
76J ARG* 3.0 31.2 + - + +
128J HIS* 3.8 30.1 - - + +
129J LEU* 4.2 11.0 - - + -
132J PHE* 3.7 37.7 - - + -
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Residues in contact with GLN 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 2.7 37.6 + - - -
17J GLU* 3.0 24.9 + - - +
20J ILE* 3.8 12.3 - - + +
21J ASN* 3.0 28.1 + - - +
24J ILE* 4.8 1.1 - - + -
69J LEU 3.0 16.3 + - - +
70J MET* 3.5 5.6 - - - +
72J LEU* 1.3 80.5 - - - +
74J ASN* 1.4 61.9 + - - +
76J ARG* 3.4 1.0 + - - +
77J GLY 3.1 2.9 + - - -
78J GLY* 2.9 47.2 + - - +
79J ARG 3.8 1.8 + - - -
80J ILE* 3.7 24.9 - - + +
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Residues in contact with ASN 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J VAL* 4.2 4.7 - - - +
70J MET 3.1 16.7 + - - +
71J LYS* 3.7 8.7 - - - +
73J GLN* 1.4 75.2 - - - +
75J GLN* 1.3 65.7 + - - +
77J GLY* 3.1 12.3 + - - -
78J GLY 3.9 13.3 - - - +
79J ARG* 3.9 12.5 + - - +
80J ILE* 4.1 21.4 + - - +
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Residues in contact with GLN 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J VAL* 3.7 13.3 - - - +
71J LYS* 2.8 49.1 + - + +
72J LEU* 3.0 31.6 + - + +
74J ASN* 1.3 72.9 - - - +
76J ARG* 1.3 66.2 + - + +
77J GLY 3.6 0.2 + - - -
128J HIS* 5.2 5.4 - - + -
132J PHE* 5.4 3.1 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J VAL* 3.9 6.0 - - - +
9J ARG* 3.5 25.6 - - - +
10J GLN 3.0 28.4 + - - +
11J ASN* 3.1 23.6 + - - +
12J TYR* 3.6 41.6 - - + +
72J LEU* 3.0 30.6 + - + +
73J GLN 4.1 0.2 - - - +
75J GLN* 1.3 81.5 - - + +
77J GLY* 1.3 61.0 + - - +
78J GLY 3.6 0.3 + - - -
126J ASP* 3.0 29.9 + - - -
128J HIS* 3.1 37.8 + - - +
129J LEU* 3.8 5.9 - - - +
----------------------------------------------------------
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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