Contacts of the helix formed by residues 42 - 71 (chain J) in PDB entry 3A68
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 VAL 42 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ARG* 3.5 2.6 + - - +
40J LYS* 4.0 5.3 + - - +
41J TYR* 1.3 79.9 - - - +
43J ASP* 1.3 65.8 + - - +
44J GLU* 3.8 5.6 - - + +
45J SER* 2.9 37.6 + - - +
46J GLU 3.0 10.6 + - - -
157J ASN* 3.8 35.9 - - + +
159J ASP* 4.9 0.2 + - - -
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Residues in contact with ASP 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ARG* 3.0 25.5 + - - +
42J VAL* 1.3 73.8 - - - +
44J GLU* 1.3 58.3 + - - +
46J GLU* 3.3 12.9 + - - +
47J SER* 2.8 37.0 + - - +
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 3.1 8.1 + - + +
43J ASP* 1.3 78.2 - - - +
45J SER* 1.3 56.6 + - - +
47J SER* 3.7 5.9 - - - -
48J ALA* 3.0 28.1 + - - +
153J VAL* 3.7 22.2 - - + +
156J LYS* 5.7 4.3 - - - +
157J ASN* 3.1 31.7 + - - +
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Residues in contact with SER 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 4.1 16.6 - - - -
42J VAL* 2.9 23.1 + - - +
44J GLU* 1.3 76.4 - - - +
46J GLU* 1.3 64.0 + - - +
48J ALA* 3.1 3.0 + - - +
49J VAL* 2.9 27.7 + - - +
153J VAL* 4.3 8.5 - - - +
154J ALA* 4.5 4.5 - - - -
157J ASN* 4.3 7.8 - - - +
159J ASP* 4.1 13.3 + - - +
162J LEU* 3.9 23.2 - - - +
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Residues in contact with GLU 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ARG* 3.6 26.3 + - - +
41J TYR* 3.8 11.9 - - + -
42J VAL 3.0 10.6 + - - +
43J ASP* 3.5 17.6 - - - +
45J SER* 1.3 75.8 - - - +
47J SER* 1.3 63.8 + - - +
49J VAL 3.3 1.2 + - - -
50J ASN* 3.1 13.6 + - - +
102J GLN* 3.0 45.0 + - - +
107J GLY* 3.4 4.5 - - - -
108J LYS* 2.7 36.6 + - - +
110J LYS* 5.7 3.5 + - - -
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Residues in contact with SER 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J ASP* 2.8 24.9 + - - +
44J GLU* 3.7 6.9 - - - -
46J GLU* 1.3 75.2 + - - +
48J ALA* 1.3 59.1 + - - +
50J ASN* 3.3 10.8 + - - +
51J GLU* 2.9 35.7 + - - +
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Residues in contact with ALA 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU 3.0 18.4 + - - +
45J SER* 3.1 4.0 + - - +
47J SER* 1.3 75.5 - - - +
49J VAL* 1.3 62.8 + - - +
51J GLU* 3.3 12.9 + - - +
52J GLN* 3.0 22.5 + - - +
150J LEU* 3.6 25.7 - - + +
153J VAL* 4.0 24.2 - - + -
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Residues in contact with VAL 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 3.3 20.4 - - - +
45J SER 2.9 12.9 + - - +
46J GLU 3.7 7.2 - - - +
47J SER 3.2 0.2 - - - -
48J ALA* 1.3 74.7 - - - +
50J ASN* 1.3 64.9 + - - +
52J GLN* 3.1 6.5 + - - +
53J ILE* 3.0 26.3 + - + +
98J LEU* 3.9 33.8 - - + +
101J TYR* 4.8 3.8 - - + -
102J GLN* 3.7 18.2 - - + +
150J LEU* 4.1 11.9 - - + -
162J LEU* 3.9 26.9 - - + -
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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
----------------------------------------------------------
46J GLU* 3.1 17.1 + - - +
47J SER* 3.6 11.2 - - - +
49J VAL* 1.3 75.9 - - - +
51J GLU* 1.3 62.8 + - - +
53J ILE* 3.4 15.2 + - - +
54J ASN* 3.2 20.4 + - - +
102J GLN* 3.1 17.9 + - - +
108J LYS 3.0 21.4 + - - -
109J VAL* 3.4 4.3 - - - -
110J LYS* 3.0 50.8 + - + +
112J GLN* 5.5 3.9 - - + +
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Residues in contact with GLU 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J SER* 2.9 19.5 + - - +
48J ALA* 3.5 13.6 - - - +
49J VAL 3.2 0.2 - - - -
50J ASN* 1.3 78.3 - - + +
52J GLN* 1.3 56.9 - - - +
54J ASN* 3.1 9.4 + - - +
55J VAL* 3.0 31.4 + - + +
112J GLN* 6.6 0.2 - - - -
146J LYS* 5.9 0.9 + - - -
14N ILE* 4.5 30.9 - - + +
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Residues in contact with GLN 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J ALA 3.0 13.1 + - - +
49J VAL 3.1 6.7 + - - +
51J GLU* 1.3 73.6 - - - +
53J ILE* 1.3 67.2 + - - +
55J VAL* 3.1 18.5 + - - +
56J GLU* 2.9 55.5 + - - +
98J LEU* 3.5 21.5 - - + -
143J THR* 3.9 5.3 + - - +
146J LYS* 3.4 28.3 - - - +
147J LEU* 3.4 29.8 - - + +
150J LEU* 3.9 17.2 - - + +
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J VAL* 3.0 24.6 + - + +
50J ASN* 3.6 26.5 - - - +
52J GLN* 1.3 75.9 - - - +
54J ASN* 1.3 59.7 + - - +
56J GLU* 3.4 2.3 + - - +
57J TYR* 2.9 29.8 + - + +
95J ALA* 3.8 12.6 - - + +
98J LEU* 3.5 28.5 - - + +
99J MET* 3.7 38.1 - - + +
102J GLN* 4.7 0.2 - - + -
109J VAL* 4.4 7.9 - - + -
110J LYS 5.9 0.7 - - - +
111J LEU* 3.8 30.1 - - + -
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Residues in contact with ASN 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J ASN 3.2 9.6 + - - +
51J GLU* 3.1 10.4 + - - +
53J ILE* 1.3 79.1 - - - +
55J VAL* 1.3 64.2 + - - +
57J TYR* 3.9 3.9 - - - +
58J ASN* 2.9 49.2 + - - +
112J GLN* 3.5 26.1 - - + +
113J SER 3.1 23.3 + - - +
114J ILE* 4.3 1.9 - - - +
14N ILE* 3.3 31.5 - - + +
15N PHE* 3.9 11.5 + - - +
61X TYR* 4.1 6.2 + - - -
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Residues in contact with VAL 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J GLU* 3.0 20.9 + - + +
52J GLN* 3.1 32.3 + - - +
54J ASN* 1.3 76.4 - - - +
56J GLU* 1.3 62.5 + - - +
58J ASN* 3.2 3.8 + - - +
59J VAL* 3.0 27.8 + - + +
143J THR* 4.2 20.4 - - + +
146J LYS* 4.1 27.8 - - + -
15N PHE* 4.1 37.9 - - + -
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Residues in contact with GLU 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLN* 2.9 45.1 + - - +
53J ILE 3.8 2.9 - - - +
55J VAL* 1.3 75.5 - - - +
57J TYR* 1.3 57.3 - - - +
59J VAL* 3.3 4.4 + - - +
60J SER* 2.9 27.9 + - - -
91J GLU* 3.1 16.4 - - - +
94J HIS* 3.6 12.7 - - + +
95J ALA* 3.8 19.3 - - + +
98J LEU* 4.0 15.0 - - + -
143J THR* 3.6 12.5 - - - +
147J LEU* 4.0 9.4 - - - +
170J TYR* 4.3 7.4 - - - -
214J CA 2.4 28.7 - - - -
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Residues in contact with TYR 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J ILE* 2.9 23.0 + - + +
54J ASN* 3.9 7.0 - - - +
55J VAL 3.3 0.2 - - - -
56J GLU* 1.3 76.2 - - - +
58J ASN* 1.3 58.6 - - - +
60J SER* 3.2 12.9 + - - -
61J TYR* 3.0 27.2 + + + +
92J ARG* 3.7 24.0 + - + -
95J ALA* 3.7 22.4 - - + +
99J MET* 4.5 6.1 - - - -
111J LEU* 4.6 1.8 - - + -
114J ILE* 3.5 26.0 - - + +
57X TYR* 5.4 12.3 - + - -
60X SER* 5.0 2.6 + - - -
61X TYR* 3.6 38.7 - + - +
64X HIS* 2.7 41.6 + + - +
88X SER* 4.6 1.2 + - - -
114X ILE* 6.3 0.2 - - + -
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Residues in contact with ASN 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J ASN* 2.9 49.0 + - - +
55J VAL 3.2 4.0 + - - +
57J TYR* 1.3 75.6 - - - +
59J VAL* 1.3 59.7 + - - +
61J TYR* 3.3 2.6 + - - +
62J VAL* 3.0 33.8 + - - +
113J SER 4.1 3.1 - - - +
114J ILE* 3.2 31.8 - - - +
115J VAL* 3.4 26.9 + - - +
15N PHE* 3.8 24.6 + - + +
17N PRO* 3.9 7.3 - - + +
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Residues in contact with VAL 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J VAL* 3.0 19.5 + - + +
56J GLU* 3.3 3.1 + - - +
58J ASN* 1.3 73.6 - - - +
60J SER* 1.3 66.8 + - - +
62J VAL* 3.3 6.5 + - - +
63J TYR* 3.0 53.4 + - + +
91J GLU* 3.5 20.9 - - - +
139J LEU* 4.8 22.0 - - + +
140J GLU* 4.3 4.7 - - - +
143J THR* 3.5 23.8 - - + +
15N PHE* 5.1 7.0 - - + -
17N PRO* 6.0 0.7 - - + -
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Residues in contact with SER 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J GLU 2.9 9.6 + - - -
57J TYR* 3.2 16.4 + - - -
59J VAL* 1.3 78.4 - - - +
61J TYR* 1.3 57.9 + - - +
63J TYR 3.3 0.5 + - - -
64J HIS 3.0 14.9 + - - -
88J SER* 2.7 51.5 + - - +
91J GLU* 3.6 18.7 - - - +
92J ARG* 3.7 18.6 - - - +
57X TYR* 5.0 2.4 + - - -
92X ARG* 4.4 3.6 + - - -
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Residues in contact with TYR 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J TYR* 3.0 13.7 + + + +
58J ASN 3.6 8.3 - - - +
59J VAL 3.2 0.2 - - - -
60J SER* 1.3 78.3 - - - +
62J VAL* 1.3 57.3 + - + +
64J HIS* 3.2 5.7 + - - +
65J ALA* 2.9 27.2 + - - +
114J ILE* 3.5 28.7 - - + -
115J VAL 3.9 4.7 - - - -
117J PRO* 3.7 30.7 - - + -
54X ASN* 4.2 5.4 + - - -
57X TYR* 3.5 51.2 - + - +
111X LEU* 3.6 19.3 - - + +
112X GLN 2.7 37.7 + - - -
114X ILE* 3.9 15.6 - - + +
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Residues in contact with VAL 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J ASN* 3.0 18.8 + - - +
59J VAL* 3.8 6.1 - - - +
61J TYR* 1.3 76.4 - - + +
63J TYR* 1.3 57.4 + - - +
65J ALA* 3.1 9.0 + - - +
66J MET* 2.9 36.3 + - + +
117J PRO* 4.2 8.1 - - + -
121J PHE* 5.0 1.3 - - + -
139J LEU* 3.6 26.5 - - + -
17N PRO* 4.2 19.5 - - + -
18N PHE* 3.6 40.2 - - + -
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Residues in contact with TYR 63 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J VAL* 3.0 35.2 + - + +
60J SER 3.7 4.0 - - - +
62J VAL* 1.3 75.7 - - - +
64J HIS* 1.3 58.2 + - - +
66J MET* 3.2 9.1 + - + -
67J PHE* 2.9 26.0 + - - +
83J PHE* 6.0 1.8 - + - -
84J PHE* 3.5 41.9 - + - +
87J SER* 3.6 23.6 - - - -
88J SER 3.8 3.6 - - - +
91J GLU* 3.7 16.6 - - + -
136J ALA* 3.6 30.0 + - + +
139J LEU* 4.2 15.3 - - + +
140J GLU* 2.5 43.0 + - - +
181J ILE* 4.1 4.2 - - + +
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Residues in contact with HIS 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J SER 3.0 8.6 + - - +
61J TYR 3.2 8.5 + - - +
63J TYR* 1.3 75.8 - - - +
65J ALA* 1.3 58.5 + - - +
67J PHE* 3.3 15.6 + + + +
68J ALA* 3.0 27.9 + - - +
85J LYS* 5.1 2.5 - - - -
88J SER* 3.5 21.3 - - - +
57X TYR* 2.6 37.3 + + - +
92X ARG* 3.7 19.7 + - + -
96X GLU* 2.7 40.0 + - + +
99X MET* 3.7 31.6 - - + +
111X LEU* 4.1 8.7 - - + -
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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
----------------------------------------------------------
61J TYR 2.9 13.5 + - - +
62J VAL 3.1 9.4 + - - +
64J HIS* 1.3 75.5 - - - +
66J MET* 1.3 61.2 + - - +
68J ALA* 3.3 7.8 + - - +
69J TYR* 3.1 17.8 + - - +
117J PRO* 3.9 16.8 - - + -
118J LEU 3.4 25.1 - - - +
119J SER* 4.5 5.1 - - - +
121J PHE* 3.8 10.1 - - + -
111X LEU* 3.7 12.2 - - + +
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Residues in contact with MET 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J VAL* 2.9 36.8 + - + +
63J TYR* 3.2 18.4 + - - +
65J ALA* 1.3 72.8 - - - +
67J PHE* 1.3 65.6 + - - +
69J TYR* 3.2 1.9 + - - +
70J PHE* 3.0 32.9 + - + -
84J PHE* 3.7 41.5 - - + -
121J PHE* 3.5 36.8 - - + -
132J ALA* 4.2 9.6 - - + +
135J LEU* 4.0 20.4 - - + -
136J ALA* 4.5 1.1 - - - +
139J LEU* 3.9 14.6 - - + -
18N PHE* 5.1 1.1 - - + -
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Residues in contact with PHE 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J TYR 2.9 14.1 + - - +
64J HIS* 3.5 25.1 - + - +
66J MET* 1.3 74.5 - - - +
68J ALA* 1.3 63.9 + - - +
70J PHE* 3.2 2.1 + - - +
71J ASP* 3.0 54.0 + - + +
81J ALA* 3.3 28.2 - - + +
82J LYS* 5.9 0.2 - - - -
84J PHE* 3.7 7.1 - - - +
85J LYS* 3.6 53.8 - - + +
96X GLU* 4.4 9.4 - - + -
99X MET* 4.1 16.2 - - + -
100X GLU* 4.0 21.3 - - + -
103X ASN* 5.5 0.4 - - - -
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Residues in contact with ALA 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J HIS 3.0 13.9 + - - +
65J ALA* 3.5 11.0 - - - +
66J MET 3.2 0.2 - - - -
67J PHE* 1.3 82.9 - - + +
69J TYR* 1.3 62.3 + - - +
72J ARG* 3.7 5.7 + - - +
99X MET* 4.0 10.1 - - + -
103X ASN* 3.0 32.8 + - - +
109X VAL* 3.8 37.2 - - + +
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Residues in contact with TYR 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J ALA 3.1 5.8 + - - +
66J MET 3.5 7.0 - - - +
67J PHE 3.1 0.4 - - - -
68J ALA* 1.3 78.1 - - - +
70J PHE* 1.3 90.6 + + - +
72J ARG* 3.1 65.0 + - - +
75J VAL* 3.6 28.9 - - + +
119J SER 3.6 10.5 - - - +
120J ASP* 3.8 4.9 - - + -
121J PHE* 3.5 41.1 - + + -
122J ASP* 3.4 33.2 + - + +
128J ASP* 4.0 13.4 + - + +
33X GLN* 6.1 0.3 - - - +
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Residues in contact with PHE 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J MET* 3.0 30.6 + - + +
67J PHE 3.8 0.2 - - - -
69J TYR* 1.3 94.1 - + - +
71J ASP* 1.3 56.9 + - - +
72J ARG 3.2 1.9 + - - -
75J VAL* 3.6 17.0 - - + -
76J ALA* 3.8 5.5 + - - -
77J LEU* 3.5 47.1 + - + +
78J ARG* 5.3 0.2 - - - -
80J LEU* 3.6 20.0 - - + -
81J ALA* 3.8 24.6 - - - +
84J PHE* 3.8 18.6 - + - -
121J PHE* 4.6 5.8 - - + -
128J ASP* 3.6 22.9 - - + -
132J ALA* 3.4 34.1 - - + -
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Residues in contact with ASP 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 2.9 35.3 + - - -
183A GLU* 4.5 2.1 - - - +
67J PHE* 3.0 45.0 + - + +
69J TYR 3.2 0.6 - - - -
70J PHE* 1.3 74.1 - - - +
72J ARG* 1.3 63.2 + - - +
76J ALA* 5.7 0.2 - - - -
81J ALA* 4.2 7.1 - - + +
100X GLU* 4.1 11.9 - - - +
103X ASN* 2.9 33.5 + - - +
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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