Contacts of the helix formed by residues 42 - 71 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ARG* 3.5 2.9 + - - +
40R LYS* 4.0 5.1 + - - +
41R TYR* 1.3 81.3 - - - +
43R ASP* 1.3 65.6 + - - +
44R GLU* 3.9 10.1 - - + +
45R SER* 3.0 31.3 + - - +
46R GLU* 3.1 9.9 + - - +
157R ASN* 3.8 31.4 - - + +
159R ASP* 4.9 0.2 + - - -
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Residues in contact with ASP 43 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ARG* 3.0 25.0 + - - +
42R VAL* 1.3 73.7 - - - +
44R GLU* 1.3 57.1 + - - +
46R GLU* 3.3 12.7 + - - +
47R SER* 2.8 36.8 + - - +
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Residues in contact with GLU 44 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R VAL* 3.2 6.9 - - + +
43R ASP* 1.3 78.7 - - - +
45R SER* 1.3 56.2 + - - +
47R SER* 3.5 6.8 + - - -
48R ALA* 3.0 27.2 + - - +
153R VAL* 3.8 20.8 - - + +
156R LYS* 6.5 0.2 - - - -
157R ASN* 2.6 36.6 + - - +
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Residues in contact with SER 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R TYR* 4.0 16.8 - - - -
42R VAL* 3.0 22.8 + - - +
44R GLU* 1.3 76.7 - - - +
46R GLU* 1.3 65.9 + - - +
48R ALA* 3.2 6.1 + - - +
49R VAL* 2.9 27.9 + - - +
153R VAL* 4.5 5.4 - - - +
154R ALA* 4.7 1.2 - - - -
157R ASN* 4.3 9.5 + - - +
159R ASP* 4.2 13.5 + - - +
162R LEU* 3.7 25.7 - - - +
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Residues in contact with GLU 46 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ARG* 3.7 24.2 + - - +
41R TYR* 3.8 12.4 - - + -
42R VAL 3.1 8.9 + - - +
43R ASP* 3.5 17.3 - - - +
45R SER* 1.3 78.6 - - - +
47R SER* 1.3 62.5 + - - +
49R VAL 3.3 1.2 + - - -
50R ASN* 3.1 25.6 + - - +
102R GLN* 3.1 35.7 + - - +
107R GLY* 3.4 6.5 - - - -
108R LYS* 2.8 34.8 + - - +
110R LYS* 5.5 2.4 + - - -
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Residues in contact with SER 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ASP* 2.8 23.8 + - - +
44R GLU* 3.8 7.6 - - - -
46R GLU* 1.3 75.3 + - - +
48R ALA* 1.3 59.2 + - - +
50R ASN* 3.2 11.2 + - - +
51R GLU* 2.9 27.3 + - - +
112R GLN* 5.4 0.2 - - - +
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Residues in contact with ALA 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLU* 3.0 19.2 + - + +
45R SER 3.2 3.8 + - - +
47R SER* 1.3 76.7 - - - +
49R VAL* 1.3 61.0 + - - +
51R GLU* 3.3 12.7 + - - +
52R GLN* 3.0 22.9 + - - +
150R LEU* 3.6 25.1 - - + +
153R VAL* 4.0 24.2 - - + -
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Residues in contact with VAL 49 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R TYR* 3.4 20.2 - - - +
45R SER 2.9 16.3 + - - +
46R GLU 3.7 4.3 - - - +
48R ALA* 1.3 74.1 - - - +
50R ASN* 1.3 65.3 + - - +
52R GLN* 3.1 6.0 + - - +
53R ILE* 3.0 25.9 + - + +
98R LEU* 3.9 32.7 - - + +
101R TYR* 4.7 4.7 - - + -
102R GLN* 3.8 20.0 - - + +
150R LEU* 4.1 13.0 - - + -
162R LEU* 3.9 26.2 - - + -
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Residues in contact with ASN 50 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R GLU* 3.1 17.8 + - - +
47R SER* 3.5 11.4 - - - +
49R VAL* 1.3 76.7 - - - +
51R GLU* 1.3 61.9 + - - +
53R ILE* 3.3 15.4 + - - +
54R ASN* 3.2 18.0 + - - +
102R GLN* 3.0 19.0 + - - +
108R LYS 3.1 20.6 + - - -
109R VAL* 3.4 4.0 - - - -
110R LYS* 3.0 45.0 + - + +
112R GLN* 3.8 14.3 - - - +
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Residues in contact with GLU 51 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 3.2 35.3 + - - +
14C ILE 6.0 1.6 - - - +
15C PHE* 6.3 1.1 - - + -
47R SER 2.9 13.9 + - - +
48R ALA* 3.4 13.8 - - - +
49R VAL 3.2 0.2 - - - -
50R ASN* 1.3 76.4 - - - +
52R GLN* 1.3 64.2 - - - +
54R ASN* 3.1 7.0 + - - +
55R VAL* 3.0 27.5 + - + +
112R GLN* 4.2 1.9 + - - -
146R LYS* 4.2 23.4 + - - +
149R ASN* 5.8 3.1 - - - +
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Residues in contact with GLN 52 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ALA 3.0 14.4 + - - +
49R VAL* 3.1 6.7 + - - +
51R GLU* 1.3 76.0 - - - +
53R ILE* 1.3 65.7 + - - +
55R VAL* 3.1 20.3 + - - +
56R GLU* 2.9 49.3 + - - +
98R LEU* 3.6 20.4 - - + -
143R THR* 4.0 3.6 - - - +
146R LYS* 3.4 30.8 - - - +
147R LEU* 3.5 29.1 - - + +
150R LEU* 3.9 18.4 - - + +
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Residues in contact with ILE 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R VAL* 3.0 24.5 + - + +
50R ASN* 3.6 25.8 - - - +
51R GLU 3.3 0.2 - - - -
52R GLN* 1.3 76.2 - - - +
54R ASN* 1.3 59.7 + - - +
56R GLU* 3.4 3.8 + - - +
57R TYR* 3.0 32.8 + - + +
95R ALA* 4.0 6.4 - - + +
98R LEU* 3.5 28.9 - - + +
99R MET* 3.7 39.0 - - + +
102R GLN* 4.7 0.7 - - + -
109R VAL* 4.4 8.3 - - + -
110R LYS 5.9 1.1 - - - +
111R LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 54 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL 3.0 17.0 - - - +
15C PHE* 3.7 9.7 + - - +
61N TYR* 4.2 7.5 + - - -
50R ASN 3.2 4.1 + - - +
51R GLU 3.1 8.8 + - - +
53R ILE* 1.3 79.3 - - - +
55R VAL* 1.3 59.5 + - - +
57R TYR* 4.4 2.9 - - - -
58R ASN* 2.9 55.2 + - - +
112R GLN* 3.1 43.8 + - + +
113R SER 3.1 25.0 + - - +
114R ILE* 4.2 2.4 - - - +
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Residues in contact with VAL 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.9 35.6 - - + -
51R GLU* 3.0 26.4 + - + +
52R GLN* 3.1 34.3 + - - +
54R ASN* 1.3 75.7 - - - +
56R GLU* 1.3 64.9 + - - +
58R ASN* 3.2 4.2 + - - +
59R VAL* 3.0 27.0 + - + +
143R THR* 4.4 17.7 - - + +
146R LYS* 4.1 28.5 - - + -
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Residues in contact with GLU 56 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R GLN* 2.9 42.1 + - - +
53R ILE 3.8 2.9 - - - +
55R VAL* 1.3 76.5 - - - +
57R TYR* 1.3 58.6 + - - +
59R VAL* 3.2 4.2 + - - +
60R SER* 2.9 27.7 + - - -
91R GLU* 3.1 16.3 - - - +
94R HIS* 3.6 13.8 - - + +
95R ALA* 3.8 19.3 - - + +
98R LEU* 3.9 16.6 - - + -
143R THR* 3.7 13.3 - - - +
147R LEU* 4.0 10.4 - - - +
170R TYR* 4.2 7.1 - - - -
214R CA 2.5 28.3 - - - -
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Residues in contact with TYR 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N TYR* 5.4 13.2 - + - -
60N SER* 5.0 2.6 + - - -
61N TYR* 3.5 39.2 - + - +
64N HIS* 2.7 41.1 + + - +
88N SER* 4.6 1.2 + - - -
114N ILE* 6.2 0.2 - - + -
53R ILE* 3.0 16.9 + - + +
54R ASN* 3.9 5.8 - - - +
56R GLU* 1.3 76.0 - - - +
58R ASN* 1.3 63.9 + - - +
60R SER* 3.3 12.6 + - - -
61R TYR* 3.0 23.7 + + + +
92R ARG* 3.6 25.1 + - + -
95R ALA* 3.8 22.0 - - + -
99R MET* 4.5 6.1 - - - -
111R LEU* 4.5 9.4 - - + -
114R ILE* 3.6 25.5 - - + +
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Residues in contact with ASN 58 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.8 27.3 + - + -
17C PRO* 3.8 9.5 - - + +
54R ASN* 2.9 52.0 + - - +
55R VAL 3.5 4.3 - - - +
57R TYR* 1.3 76.9 - - - +
59R VAL* 1.3 62.3 + - - +
61R TYR* 3.1 4.2 + - - +
62R VAL* 3.0 28.2 + - - +
113R SER 4.1 6.5 + - - -
114R ILE* 3.5 23.2 - - - +
115R VAL* 3.5 23.4 + - - +
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Residues in contact with VAL 59 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 4.9 7.9 - - + -
17C PRO* 5.8 0.7 - - + -
55R VAL* 3.0 20.3 + - + +
56R GLU* 3.2 6.5 + - - +
58R ASN* 1.3 75.3 - - - +
60R SER* 1.3 63.6 + - - +
62R VAL* 3.2 7.5 + - - +
63R TYR* 3.0 52.4 + - + -
91R GLU* 3.6 16.4 - - - +
139R LEU* 4.9 22.7 - - + +
140R GLU* 4.3 4.7 - - - +
142R LEU* 6.4 0.2 - - + -
143R THR* 3.5 23.8 - - + +
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Residues in contact with SER 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N TYR* 4.9 2.8 + - - -
92N ARG* 4.5 3.6 + - - -
56R GLU 2.9 10.8 + - - -
57R TYR* 3.3 16.1 + - - -
59R VAL* 1.3 75.6 - - - +
61R TYR* 1.3 57.4 + - - +
63R TYR 3.4 0.5 + - - -
64R HIS 3.0 14.9 + - - -
88R SER* 2.7 51.9 + - - +
91R GLU* 3.5 19.8 - - - +
92R ARG* 3.7 18.6 + - - +
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Residues in contact with TYR 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N ASN* 4.2 4.7 + - - -
57N TYR* 3.6 45.8 - + - +
111N LEU* 3.6 20.0 - - + +
112N GLN 2.6 37.5 + - - -
113N SER* 5.1 0.2 - - - -
114N ILE* 3.7 21.8 - - + +
57R TYR* 3.0 14.3 + + + +
58R ASN 3.1 8.5 + - - +
60R SER* 1.3 74.7 - - - +
62R VAL* 1.3 65.9 + - + +
64R HIS* 3.1 5.2 + - - +
65R ALA* 3.0 22.0 + - - +
114R ILE* 3.5 27.6 - - + -
115R VAL 3.9 5.2 - - - -
117R PRO* 3.6 31.8 - - + +
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Residues in contact with VAL 62 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 4.0 23.6 - - + -
18C PHE* 3.7 37.5 - - + -
58R ASN 3.0 19.2 + - - +
59R VAL* 3.7 7.4 - - - +
61R TYR* 1.3 76.2 - - + +
63R TYR* 1.3 57.1 + - - +
65R ALA* 3.1 4.2 + - - +
66R MET* 2.9 36.5 + - + +
117R PRO* 4.2 12.6 - - + -
121R PHE* 5.1 0.4 - - + -
135R LEU* 5.1 0.2 - - + -
139R LEU* 3.5 30.5 - - + -
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Residues in contact with TYR 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R VAL* 3.0 29.5 + - + +
60R SER 3.7 4.7 - - - +
62R VAL* 1.3 76.0 - - - +
64R HIS* 1.3 57.0 + - - +
66R MET* 3.2 14.7 + - - +
67R PHE* 2.9 25.5 + - - +
83R PHE* 6.0 1.1 - + - -
84R PHE* 3.5 41.3 - + - +
87R SER* 3.5 24.9 - - - -
88R SER 3.7 4.3 - - - +
91R GLU* 3.6 22.2 - - + -
136R ALA* 3.6 31.3 + - + +
139R LEU* 4.4 10.0 - - + +
140R GLU* 2.5 41.5 + - - +
181R ILE* 4.2 4.5 - - + +
----------------------------------------------------------
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Residues in contact with HIS 64 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N TYR* 2.7 35.8 + + - +
92N ARG* 3.7 18.2 + - + -
96N GLU* 2.7 41.2 + - + +
99N MET* 3.6 27.8 - - + +
111N LEU* 4.1 7.9 - - + -
60R SER 3.0 7.8 + - - +
61R TYR* 3.1 9.4 + - - +
63R TYR* 1.3 76.0 - - - +
65R ALA* 1.3 58.4 + - - +
67R PHE* 3.3 15.9 + + + +
68R ALA* 3.0 27.5 + - - +
85R LYS* 5.1 2.2 - - + -
88R SER* 3.5 21.3 - - - +
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Residues in contact with ALA 65 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU* 3.7 13.3 - - + +
61R TYR 3.0 12.4 + - - +
62R VAL 3.4 8.7 - - - +
64R HIS* 1.3 76.8 - - - +
66R MET* 1.3 61.8 + - - +
68R ALA* 3.2 7.0 + - - +
69R TYR* 3.1 17.7 + - - +
117R PRO* 3.9 17.3 - - + -
118R LEU 3.4 24.7 - - - +
119R SER* 4.5 4.4 - - - +
121R PHE* 3.7 10.3 - - + -
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Residues in contact with MET 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R VAL* 2.9 26.2 + - + +
63R TYR* 3.6 30.7 - - - +
65R ALA* 1.3 74.7 - - - +
67R PHE* 1.3 65.4 + - - +
69R TYR* 3.2 1.7 + - - +
70R PHE* 3.1 31.2 + - + -
84R PHE* 3.4 30.5 - - + -
121R PHE* 3.4 28.3 - - + -
132R ALA* 3.2 42.8 - - + +
135R LEU* 4.3 16.8 - - + -
136R ALA* 4.6 1.1 - - - +
139R LEU* 4.8 0.9 - - - -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N GLU* 4.4 9.2 - - + -
99N MET* 4.1 16.4 - - + -
100N GLU* 4.0 20.2 - - + -
103N ASN* 5.5 0.2 - - - -
63R TYR 2.9 13.9 + - - +
64R HIS* 3.4 24.7 - + - +
66R MET* 1.3 77.6 - - - +
68R ALA* 1.3 69.3 + - - +
70R PHE 3.3 1.0 + - - -
71R ASP* 3.0 48.3 + - + +
81R ALA* 3.3 28.6 - - + +
82R LYS* 5.8 0.2 - - - -
84R PHE* 3.6 8.1 - - - +
85R LYS* 3.6 54.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99N MET* 3.9 9.9 - - + -
103N ASN* 2.9 27.5 + - - +
109N VAL* 3.7 39.5 - - + +
64R HIS 3.0 13.8 + - - +
65R ALA* 3.6 10.5 - - - +
66R MET 3.2 0.4 - - - -
67R PHE* 1.3 82.2 - - + +
69R TYR* 1.3 61.3 + - - +
72R ARG* 3.7 9.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R ALA 3.1 5.8 + - - +
66R MET 3.6 7.0 - - - +
67R PHE 3.2 0.2 - - - -
68R ALA* 1.3 77.9 - - - +
70R PHE* 1.3 88.8 + + - +
72R ARG* 3.1 60.8 + - - +
75R VAL* 3.6 33.7 - - + +
119R SER 3.7 10.1 + - - +
120R ASP* 3.9 4.9 - - + -
121R PHE* 3.6 46.7 - + + -
122R ASP* 3.3 31.1 - - + +
128R ASP* 4.2 8.8 + - + +
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Residues in contact with PHE 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R MET* 3.1 29.9 + - + +
69R TYR* 1.3 90.8 - + - +
71R ASP* 1.3 58.3 + - - +
72R ARG 3.3 1.9 + - - -
75R VAL* 3.6 16.8 - - + -
76R ALA* 3.8 5.2 + - - -
77R LEU* 3.5 39.7 + - + +
78R ARG* 5.2 0.3 - - - -
80R LEU* 3.6 22.0 - - + -
81R ALA* 3.8 24.2 - - - +
84R PHE* 3.7 18.4 - + - -
121R PHE* 4.5 6.3 - - + -
128R ASP* 3.6 29.8 - - + -
132R ALA* 3.4 35.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J LYS* 2.9 33.8 + - - -
183J GLU* 4.5 1.9 - - - +
100N GLU* 4.1 13.3 - - - +
103N ASN* 3.0 31.9 + - - +
67R PHE* 3.0 46.8 + - + +
69R TYR 3.1 0.6 - - - -
70R PHE* 1.3 73.5 - - - +
72R ARG* 1.3 62.8 + - - +
76R ALA* 5.7 0.2 - - - -
81R ALA* 3.9 7.6 - - + +
----------------------------------------------------------
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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