Contacts of the helix formed by residues 91 - 122 (chain B) in PDB entry 1JQO
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 ALA 91 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 4.1 1.0 + - - -
90B LEU* 1.3 72.0 - - - +
92B PRO* 1.3 76.9 - - + +
93B ALA* 4.5 4.5 - - + +
94B ASP* 2.8 33.4 + - - +
95B ALA 2.8 9.7 + - - -
922B GLN 4.8 8.4 + - - +
924B PRO* 3.8 27.8 - - + +
925B LEU* 5.1 1.8 - - - +
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Residues in contact with PRO 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU 3.5 4.4 - - - +
91B ALA* 1.3 84.5 - - + +
93B ALA* 1.3 61.8 + - - +
95B ALA* 3.4 7.7 + - + +
96B ILE* 3.1 26.5 + - - +
911B ARG* 6.2 2.5 - - - +
939B VAL* 3.7 14.8 - - + -
949B PRO* 3.8 21.8 - - + -
950B GLY* 3.5 24.9 - - - +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 2.9 3.9 + - + +
92B PRO* 1.3 78.0 - - - +
94B ASP* 1.3 69.3 + - - +
96B ILE* 3.1 15.9 + - - +
97B LEU* 3.1 14.6 + - + +
926B SER* 6.1 1.3 - - - -
928B GLU* 5.8 7.6 - - - -
936B ALA* 4.6 15.5 - - - +
938B LEU* 3.4 23.5 - - + +
939B VAL* 3.4 16.8 - - + +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.8 2.7 - - + +
90B LEU* 4.4 3.4 - - + -
91B ALA* 2.8 18.8 + - - +
93B ALA* 1.3 73.0 - - - +
95B ALA* 1.3 59.3 + - - +
97B LEU* 4.2 7.2 - - - -
98B VAL* 2.8 40.7 + - + +
924B PRO* 3.4 22.7 - - - +
925B LEU* 2.6 36.4 + - + +
926B SER* 2.6 37.8 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU 4.9 1.1 - - - +
90B LEU* 4.3 15.9 - - + +
91B ALA 2.8 11.2 + - - +
92B PRO* 3.6 14.1 - - + +
93B ALA 3.2 0.2 - - - -
94B ASP* 1.3 76.4 - - - +
96B ILE* 1.3 61.1 + - - +
99B ALA* 3.1 23.7 + - - +
904B PHE* 3.4 31.2 - - + -
911B ARG* 6.0 2.9 - - - +
950B GLY* 5.2 1.8 - - - +
954B THR* 3.8 13.4 + - + +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO 3.1 16.4 - - - +
93B ALA 3.2 6.1 - - - +
95B ALA* 1.3 74.4 - - - +
97B LEU* 1.3 57.1 + - + +
99B ALA* 2.7 10.2 + - - +
100B SER* 2.7 39.4 + - - +
229B GLU* 5.9 0.2 - - - +
230B ILE* 6.3 0.2 - - + -
938B LEU* 3.4 33.2 - - + -
939B VAL* 4.9 5.2 - - + -
950B GLY* 3.8 8.3 - - - +
953B ASP* 3.6 33.2 - - + +
954B THR* 3.2 24.0 - - - +
957B LEU* 3.6 12.7 - - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 3.2 41.1 - - + +
57B LEU* 3.7 15.0 - - + -
93B ALA* 3.4 14.8 - - + +
94B ASP* 3.6 8.1 - - - +
96B ILE* 1.3 81.9 - - + +
98B VAL* 1.3 54.7 + - - +
100B SER* 3.8 4.8 - - - +
101B SER* 2.7 41.7 + - - +
225B PHE* 4.4 13.4 - - + -
926B SER* 3.3 25.8 - - - +
928B GLU 6.5 0.2 - - - -
938B LEU* 3.7 21.8 - - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.6 20.2 - - + -
60B PHE* 3.4 42.8 - - + -
61B VAL* 4.7 10.0 - - + +
64B CYS* 4.9 2.7 - - - -
87B LEU* 4.3 13.7 - - + -
90B LEU* 4.3 5.6 - - + -
94B ASP* 2.8 28.0 + - + +
95B ALA 4.1 3.4 - - - +
97B LEU* 1.3 72.7 - - - +
99B ALA* 1.3 60.6 + - - +
101B SER* 4.0 6.0 - - - -
102B ILE* 3.5 33.2 + - + +
904B PHE* 4.4 5.6 - - + -
925B LEU* 5.3 0.4 - - + -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 3.1 18.2 + - - +
96B ILE* 2.7 12.3 + - - +
98B VAL* 1.3 72.0 - - - +
100B SER* 1.3 64.7 + - - +
102B ILE* 3.6 3.1 + - - +
103B LEU* 3.1 20.6 + - - +
901B LEU* 4.4 10.5 - - + +
904B PHE* 4.2 15.9 - - + -
954B THR* 4.4 8.7 - - + +
957B LEU* 3.3 26.7 - - + +
958B THR* 5.0 4.5 - - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 2.7 22.0 + - - +
97B LEU* 3.8 7.0 - - - -
99B ALA* 1.3 71.3 - - - +
101B SER* 1.3 57.2 + - - +
103B LEU* 2.7 10.6 + - - +
104B HIS* 2.6 41.7 + - - +
225B PHE* 4.3 8.3 - - - -
229B GLU* 3.2 30.1 + - - -
957B LEU* 3.2 19.9 - - - +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.7 21.9 - - - -
49B LEU* 4.0 22.0 - - - +
57B LEU* 5.4 0.7 - - - +
61B VAL* 4.2 21.6 - - - +
97B LEU 2.7 29.7 + - - -
98B VAL* 4.0 5.2 - - - -
100B SER* 1.3 72.5 - - - +
102B ILE* 1.3 52.2 + - - +
103B LEU 2.9 0.5 + - - -
104B HIS* 3.1 0.9 + - - -
105B MET* 2.7 42.7 + - - +
225B PHE* 4.0 7.1 - - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.3 13.2 - - + +
64B CYS* 5.1 5.8 - - + -
98B VAL* 3.5 26.6 + - + +
99B ALA 3.6 4.8 + - - +
100B SER 3.4 0.2 - - - -
101B SER* 1.3 78.5 - - - +
103B LEU* 1.3 56.4 + - - +
105B MET* 3.9 9.6 - - - +
106B LEU* 3.1 27.4 + - + +
897B TYR* 3.6 35.4 - - + +
900B THR* 3.6 33.4 - - + -
901B LEU* 3.6 33.7 - - + -
904B PHE* 5.9 3.1 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA 3.1 13.9 + - - +
100B SER* 2.7 12.8 + - - +
102B ILE* 1.3 74.7 - - - +
104B HIS* 1.3 64.1 + - + +
105B MET 3.1 0.9 - - - -
106B LEU* 3.3 2.8 + - - +
107B ASN* 2.9 30.1 + - + +
229B GLU* 4.4 29.4 - - + -
901B LEU* 5.2 0.4 - - - -
957B LEU* 4.5 17.3 - - + +
960B LYS* 4.0 22.0 - - + +
961B GLY* 3.3 35.0 - - - +
964B ALA* 4.5 9.9 - - + -
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.6 20.9 - + + -
100B SER 2.6 22.6 + - - +
103B LEU* 1.3 77.5 - - + +
105B MET* 1.3 61.3 + - - +
107B ASN* 3.5 11.6 + - - +
108B LEU* 3.2 29.5 + - + +
186B LEU* 3.7 21.9 - - + +
221B ILE* 6.0 0.4 - - + -
224B ALA* 3.1 31.6 + - + +
225B PHE* 3.3 29.5 - + + -
229B GLU* 2.7 42.5 + - + +
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.9 25.5 - - + +
45B PHE* 3.4 24.2 - - + -
46B LEU* 3.3 36.6 - - + -
61B VAL* 4.0 18.6 - - + -
101B SER 2.7 31.7 + - - +
102B ILE* 3.9 4.5 - - - +
104B HIS* 1.3 68.6 - - - +
106B LEU* 1.3 68.7 + - - +
107B ASN 3.0 0.9 - - - -
108B LEU* 2.8 25.2 + - - +
109B ALA* 3.0 10.8 + - - +
897B TYR* 3.2 43.1 - - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE 3.1 11.7 + - - +
103B LEU* 3.7 3.8 - - - +
105B MET* 1.3 79.5 - - - +
107B ASN* 1.3 64.8 + - - +
109B ALA* 3.1 19.8 + - + +
110B ASN* 3.0 13.9 + - - -
894B ARG* 3.7 27.0 + - + +
897B TYR* 3.2 34.8 - - + -
898B ILE* 4.0 13.9 - - + +
901B LEU* 3.7 21.1 - - + -
961B GLY 3.6 23.6 - - - +
964B ALA* 5.1 1.1 - - + -
965B GLY* 3.8 22.0 - - - +
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 2.9 22.1 + - + +
104B HIS* 3.5 13.8 + - - +
106B LEU* 1.3 75.5 - - - +
108B LEU* 1.3 66.5 + - - +
110B ASN* 2.8 33.9 + - - +
111B LEU* 3.3 12.1 + - - +
186B LEU* 4.3 19.3 - - + +
190B ASN* 3.2 40.0 - - - +
193B ILE* 5.8 0.8 - - - +
964B ALA* 4.8 7.4 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.5 46.7 - - + +
42B VAL* 4.6 6.1 - - + +
45B PHE* 3.9 35.4 - - + -
104B HIS 3.2 17.5 + - - +
105B MET* 2.8 16.3 + - - +
107B ASN* 1.3 76.6 - - - +
109B ALA* 1.3 54.2 + - - +
111B LEU* 2.6 41.4 + - + +
112B ALA* 2.8 13.1 + - - +
193B ILE* 4.3 9.9 - - + -
221B ILE* 4.2 18.2 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 5.0 9.5 - - - +
42B VAL* 5.7 6.6 - - + +
105B MET 3.0 7.9 + - - +
106B LEU* 3.1 18.2 - - + +
108B LEU* 1.3 75.2 - - - +
110B ASN* 1.3 56.4 + - - +
112B ALA* 3.6 7.0 + - - +
113B GLU* 3.1 30.5 + - - +
893B LEU* 5.1 14.4 - - + -
894B ARG* 3.8 23.7 + - + +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.0 21.8 + - - -
107B ASN* 2.8 23.4 + - - +
109B ALA* 1.3 76.3 - - - +
111B LEU* 1.3 58.2 + - + +
113B GLU* 3.7 6.3 + - - +
114B GLU* 3.1 35.4 + - - +
894B ARG* 3.1 20.6 + - - +
964B ALA* 3.5 25.9 + - - +
965B GLY* 5.2 0.4 - - - -
967B GLN* 3.3 26.6 + - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.1 5.8 - - + -
107B ASN* 3.3 10.3 + - - +
108B LEU* 2.6 30.1 + - + +
110B ASN* 1.3 69.8 - - + +
112B ALA* 1.3 63.6 + - - +
113B GLU 3.0 1.3 - - - -
114B GLU* 3.0 23.1 + - - +
115B VAL* 3.2 18.2 + - - +
190B ASN* 3.9 29.4 - - + +
193B ILE* 3.9 40.4 - - + -
194B ARG* 3.5 39.4 - - + +
197B LEU* 5.1 1.3 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.7 29.7 - - + +
38B ASP* 3.7 22.2 - - - +
41B LEU* 4.0 10.0 - - + +
108B LEU 2.8 15.3 + - - +
109B ALA* 4.1 5.8 - - - +
111B LEU* 1.3 73.3 - - - +
113B GLU* 1.3 57.2 + - - +
115B VAL* 3.5 8.0 + - - +
116B GLN* 2.9 31.9 + - - +
197B LEU* 4.3 2.7 - - - -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 5.1 6.3 + - - +
109B ALA 3.1 14.3 + - - +
110B ASN* 3.8 5.9 - - - +
111B LEU 3.0 0.8 - - - -
112B ALA* 1.3 77.5 - - - +
114B GLU* 1.3 61.6 + - + +
115B VAL 3.2 0.4 - - - -
116B GLN* 3.7 7.5 - - + +
117B ILE* 3.0 37.4 + - + +
886B PHE* 5.2 12.7 - - + -
887B LEU* 5.9 3.3 - - - +
890B GLY* 5.7 4.7 - - - -
894B ARG* 2.5 41.5 + - - -
967B GLN* 3.6 12.4 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.1 25.8 + - - +
111B LEU* 3.0 17.4 + - - +
113B GLU* 1.3 77.9 - - + +
115B VAL* 1.3 61.6 + - + +
117B ILE* 3.7 6.4 + - - +
118B ALA* 3.4 19.8 + - - +
194B ARG* 2.7 43.3 + - - -
678B GLU* 5.6 0.5 - - - +
683B GLU* 4.5 0.7 - - - +
685B HIS* 4.5 13.3 - - + -
686B LEU* 3.9 19.1 - - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.8 23.6 - - + -
111B LEU 3.2 15.7 - - - +
112B ALA* 3.7 4.7 - - - +
113B GLU 3.2 0.2 - - - -
114B GLU* 1.3 75.3 - - + +
116B GLN* 1.3 67.1 + - - +
117B ILE 2.9 3.4 + - - -
118B ALA* 3.1 4.6 + - + +
119B HIS* 2.9 49.9 + - + +
194B ARG* 4.7 15.9 - - + +
197B LEU* 3.7 30.1 - - + -
198B THR* 4.4 9.6 - - - +
685B HIS* 6.2 0.2 - - - -
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE 3.5 18.3 + - - +
36B GLU* 3.7 9.2 - - - +
37B TYR* 3.6 26.1 - - + -
38B ASP* 3.6 21.3 - - - +
112B ALA 2.9 18.1 + - - +
113B GLU* 3.7 11.2 - - - +
115B VAL* 1.3 77.9 - - - +
117B ILE* 1.3 55.4 + - - +
119B HIS* 5.0 0.8 - - - +
120B ARG* 3.1 37.4 + - - +
886B PHE* 4.2 17.2 - - + -
----------------------------------------------------------
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU* 3.0 23.1 + - + +
114B GLU* 3.8 7.2 - - - +
115B VAL 3.0 0.8 - - - -
116B GLN* 1.3 75.4 - - - +
118B ALA* 1.3 55.2 + - - +
120B ARG* 3.3 16.6 + - - +
121B ARG* 2.6 75.5 + - + +
886B PHE* 3.2 37.7 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 3.4 10.5 + - - +
115B VAL* 3.1 9.0 + - + +
117B ILE* 1.3 79.1 - - - +
119B HIS* 1.3 62.1 + - - +
121B ARG* 2.8 4.9 + - - -
122B ARG* 2.6 39.8 + - + +
685B HIS* 4.3 25.1 - - + +
----------------------------------------------------------
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.4 26.5 - - - +
115B VAL* 2.9 27.0 + - + +
116B GLN* 5.0 1.6 - - - +
118B ALA* 1.3 79.6 - - - +
120B ARG* 1.3 53.2 + - - +
122B ARG* 3.8 31.6 + - - +
123B ASN* 2.6 30.1 + - - +
198B THR* 3.8 39.7 + - + -
201B ASN* 3.6 30.5 + - + +
203B LYS* 6.5 0.4 - - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 3.1 30.6 + - - +
117B ILE* 3.3 22.1 + - - +
118B ALA 3.0 0.6 - - - -
119B HIS* 1.3 76.7 - - - +
121B ARG* 1.3 76.6 + - - +
122B ARG 3.4 0.2 - - - -
123B ASN* 3.8 15.8 - - - +
886B PHE* 3.4 43.5 - - - +
----------------------------------------------------------
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 2.6 45.0 + - + +
118B ALA* 3.7 4.5 - - - +
120B ARG* 1.3 83.9 - - - +
122B ARG* 1.3 54.4 + - - +
123B ASN 2.6 24.3 + - - -
689B GLN* 3.1 41.7 + - - +
693B ARG* 3.8 22.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 3.7 46.3 + - - +
206A THR* 5.5 10.7 - - + +
118B ALA* 2.6 23.2 + - + +
119B HIS* 3.8 38.9 + - - +
120B ARG 3.4 0.2 - - - -
121B ARG* 1.3 70.8 - - - +
123B ASN* 1.3 70.6 + - - +
201B ASN 5.6 1.0 + - - -
203B LYS* 6.3 0.8 - - - +
----------------------------------------------------------
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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