Contacts of the helix formed by residues 89 - 115 (chain B) in PDB entry 2F3M
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 THR 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 1.3 83.0 - - + +
90B GLU* 1.3 65.3 + - - +
91B GLU* 2.9 19.6 + - - +
92B GLU* 3.1 33.5 + - + +
93B LYS* 3.2 22.0 + - - +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 4.7 10.5 - - + +
78A TYR* 3.5 22.5 - - + +
81A ARG* 3.1 45.7 + - - +
89B THR* 1.3 74.9 + - - +
91B GLU* 1.3 66.0 + - - +
93B LYS* 3.0 16.6 + - - +
94B ILE* 3.0 22.9 + - + +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.5 30.9 + - - +
89B THR* 2.9 7.6 + - - +
90B GLU* 1.3 78.2 - - - +
92B GLU* 1.3 63.6 + - + +
94B ILE* 3.3 10.4 + - - +
95B ARG* 3.2 46.0 + - - +
148B ALA 5.2 0.2 - - - -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY* 3.7 7.6 - - - -
88B GLU* 2.9 38.7 + - - +
89B THR* 3.1 40.5 + - + +
91B GLU* 1.3 76.9 - - + +
93B LYS* 1.3 58.0 + - - +
95B ARG* 3.5 2.6 + - - +
96B VAL* 3.0 32.7 + - - +
148B ALA* 3.9 27.8 - - + +
149B GLY* 5.4 2.7 - - - -
150B ASN 5.3 2.4 + - - -
151B LYS* 4.6 19.1 + - - +
153B THR* 4.6 5.5 - - - +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.9 40.4 - - - +
86B CYS 4.2 9.6 - - - +
87B GLY 3.7 22.9 - - - +
88B GLU 4.0 8.2 + - - -
89B THR 3.2 14.5 + - - +
90B GLU* 3.0 11.4 + - - +
92B GLU* 1.3 76.7 - - - +
94B ILE* 1.3 60.8 + - - +
96B VAL* 3.2 7.4 + - - +
97B ASP* 2.8 36.3 + - - +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.2 37.7 - - + +
68A LYS 5.4 1.1 - - - +
69A ILE* 3.9 24.5 - - + -
74A ALA* 6.2 0.7 - - + -
78A TYR* 3.7 23.6 - - + -
81A ARG* 3.9 9.2 - - - +
90B GLU* 3.0 26.7 + - + +
91B GLU* 3.7 12.3 - - - +
93B LYS* 1.3 75.0 - - - +
95B ARG* 1.3 68.6 + - + +
97B ASP* 3.1 4.9 + - - +
98B ILE* 2.9 37.0 + - + +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.3 1.4 + - - -
91B GLU* 3.2 33.1 + - - +
92B GLU 3.8 4.0 - - - +
94B ILE* 1.3 84.5 - - + +
96B VAL* 1.3 61.4 + - - +
98B ILE* 3.2 4.5 + - + +
99B LEU* 2.9 30.6 + - + +
140B PHE* 2.8 67.3 + - + -
141B LEU* 4.6 0.8 - - - +
144B ARG* 3.4 34.6 - - - +
147B PHE 2.8 32.9 + - - +
148B ALA* 3.4 21.5 + - - -
155B VAL* 5.5 0.2 - - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 6.1 0.2 - - - -
86B CYS 4.0 22.7 - - - +
87B GLY* 4.6 1.3 - - - -
92B GLU 3.0 20.7 + - - +
93B LYS* 3.4 9.4 - - - +
95B ARG* 1.3 74.0 - - - +
97B ASP* 1.3 65.2 + - - +
99B LEU 3.5 0.2 + - - -
100B GLU* 2.9 34.5 + - - +
148B ALA* 4.4 7.0 - - + -
153B THR* 4.3 11.0 - - - +
154B PHE* 3.6 32.1 - - + -
155B VAL* 3.5 28.3 - - + +
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN 5.8 0.2 - - - -
74A ALA* 3.6 23.2 - - + +
77A CYS* 3.6 19.6 - - - +
81A ARG* 3.2 31.4 + - - -
100A GLU* 5.8 2.7 - - - +
93B LYS* 2.8 19.4 + - - +
94B ILE* 3.6 7.6 - - - +
96B VAL* 1.3 77.6 - - - +
98B ILE* 1.3 60.2 + - - +
100B GLU* 3.5 15.3 - - - +
101B ASN* 2.7 32.1 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.2 9.6 - - + +
56A PHE* 3.9 30.1 - - + -
68A LYS 4.6 5.2 - - - +
69A ILE* 4.5 6.5 - - + -
70A THR* 3.7 38.1 - - - +
71A GLN* 3.7 11.6 - - + +
74A ALA* 4.1 9.6 - - + -
94B ILE* 2.9 35.3 + - + +
95B ARG* 3.7 9.4 - - + +
97B ASP* 1.3 75.4 - - - +
99B LEU* 1.3 53.6 + - - +
101B ASN* 3.0 4.7 + - - -
102B GLN* 2.7 36.0 + - + +
140B PHE* 5.2 8.3 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.1 16.4 - - + -
95B ARG 2.9 17.0 + - - +
98B ILE* 1.3 73.3 - - - +
100B GLU* 1.3 64.2 + - - +
102B GLN* 3.9 4.3 - - + -
103B THR* 2.8 30.3 + - - +
137B TYR* 4.1 19.5 - - + -
140B PHE* 3.5 35.9 - - + -
147B PHE* 3.3 37.5 - - + -
155B VAL* 3.9 26.0 - - + -
159B VAL* 4.0 12.1 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.6 2.4 - - - +
100A GLU* 4.9 15.8 - - - +
101A ASN* 5.0 2.4 + - - -
73B ASN* 3.1 59.7 + - - +
77B CYS* 4.9 3.8 - - - +
96B VAL* 2.9 17.8 + - - +
97B ASP* 3.5 24.8 + - - +
99B LEU* 1.3 77.9 - - - +
101B ASN* 1.3 65.1 + - - +
103B THR* 3.4 10.6 + - - -
104B MET* 3.8 5.0 + - - +
154B PHE* 4.0 21.7 - - + -
155B VAL* 3.8 11.3 - - + +
158B LEU* 4.2 5.2 - - - -
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.2 28.1 - - + +
73A ASN* 3.8 36.8 + - - +
74A ALA* 4.1 6.9 - - - +
100A GLU* 5.1 3.0 + - - +
101A ASN* 4.5 8.3 - - - +
104A MET* 6.0 0.9 - - - +
1218A GTD 5.2 0.9 - - - +
73B ASN* 4.8 3.1 + - - -
97B ASP* 2.7 24.5 + - - +
98B ILE 3.0 2.0 + - - -
100B GLU* 1.3 86.6 + - - +
102B GLN* 1.3 65.9 + - - +
103B THR 3.3 0.7 - - - -
104B MET* 3.3 7.1 + - - +
105B ASP* 3.0 27.2 + - - +
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.4 54.1 - - + +
58A ASN* 4.7 4.9 + - - +
71A GLN* 3.2 24.6 + - - +
98B ILE* 2.7 26.2 + - + +
99B LEU* 3.9 10.1 - - + +
101B ASN* 1.3 71.7 - - - +
103B THR* 1.3 63.5 + - - +
105B ASP* 3.2 8.4 + - - +
106B ASN* 3.1 53.4 + - - +
136B LEU* 5.6 3.2 - - - +
137B TYR* 3.8 8.5 - - + +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 2.8 27.0 + - - +
100B GLU 3.4 6.6 + - - -
102B GLN* 1.3 72.7 - - - +
104B MET* 1.3 60.3 + - - +
106B ASN* 3.2 3.5 + - - +
107B HIS* 2.8 36.2 + - - +
137B TYR* 3.6 19.3 - - + +
158B LEU* 3.6 28.7 - - + +
159B VAL* 3.9 40.2 - - + +
162B VAL* 3.8 8.5 - - + +
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.0 33.9 - - + -
72B SER* 4.8 4.5 - - - -
73B ASN* 4.5 12.1 - - - +
100B GLU 3.8 11.4 + - - +
101B ASN* 3.3 11.4 + - - +
102B GLN 3.3 0.2 - - - -
103B THR* 1.3 80.8 + - - +
105B ASP* 1.3 60.8 + - - +
107B HIS* 3.4 14.8 + - + -
108B MET* 2.9 48.2 + - + +
158B LEU* 6.5 0.2 - - - -
2218B GTD 4.5 22.9 - - + +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.8 3.3 + - - -
71A GLN* 3.1 12.2 + - - +
104A MET* 5.4 2.6 - - - +
1218A GTD 2.9 33.7 + - - +
101B ASN 3.0 15.4 + - - +
102B GLN* 3.5 12.3 - - - +
103B THR 3.1 0.4 - - - -
104B MET* 1.3 77.2 - - - +
106B ASN* 1.3 67.8 + - - +
108B MET* 3.1 23.0 + - - +
109B GLN* 2.9 39.4 + - - +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 3.1 28.6 + - - +
103B THR 3.8 5.4 - - - +
105B ASP* 1.3 74.9 - - - +
107B HIS* 1.3 56.4 + - - +
109B GLN* 3.0 27.3 + - - +
110B LEU* 3.1 26.7 + - - +
126B TYR* 4.1 3.8 + - - -
133B LYS* 4.1 21.2 + - + +
137B TYR* 2.4 37.3 + - - +
162B VAL* 4.6 13.7 - - + -
166B HIS* 4.6 7.1 - - + -
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY* 4.4 13.5 - - - -
12B LEU* 3.8 27.8 - - + +
103B THR 2.8 17.0 + - - +
104B MET* 3.6 15.7 - - + +
106B ASN* 1.3 73.9 - - - +
108B MET* 1.3 68.5 + - - +
109B GLN 3.2 0.2 + - - -
110B LEU* 3.2 6.9 + - + +
111B GLY 2.9 19.2 + - - -
161B ASP* 4.2 9.2 + - - -
162B VAL* 4.2 12.4 - - + +
165B LEU* 3.9 26.7 - - + +
166B HIS* 6.1 0.2 - - - -
207B VAL* 6.1 0.4 - - + -
208B PHE* 4.1 13.4 - + - -
2218B GTD 3.4 30.4 + - + +
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 6.4 1.8 - - + -
108A MET* 3.3 40.4 - - + +
104B MET* 2.9 36.4 + - + +
105B ASP* 3.5 26.9 - - - +
107B HIS* 1.3 72.8 - - - +
109B GLN* 1.3 54.8 + - + +
111B GLY 3.2 1.7 + - - -
112B MET* 2.7 55.8 + - + +
2218B GTD 3.9 14.7 + - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 2.9 29.2 + - - +
106B ASN* 3.0 28.4 + - - +
107B HIS 3.1 0.2 - - - -
108B MET* 1.3 75.6 - - + +
110B LEU* 1.3 67.1 + - - +
112B MET* 3.3 33.8 + - + +
113B ILE* 3.6 8.0 + - - +
126B TYR* 3.8 11.0 - - + -
133B LYS* 2.9 33.2 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN 3.1 8.9 + - - +
107B HIS* 3.6 9.0 - - + +
109B GLN* 1.3 79.1 - - - +
111B GLY* 1.3 63.9 + - - +
112B MET 3.1 1.2 + - - -
113B ILE* 3.2 7.1 + - + +
114B CYS* 3.1 34.0 + - - -
126B TYR* 3.2 36.0 + - + +
165B LEU* 4.1 30.1 - - + +
166B HIS* 3.9 22.0 - - + +
169B PHE* 4.3 15.9 - - + -
208B PHE* 4.1 19.5 - - + -
214B TRP* 5.2 5.2 - - + -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B HIS 2.9 13.7 + - - -
108B MET 3.5 3.8 - - - -
110B LEU* 1.3 75.9 - - - +
112B MET* 1.3 61.0 + - - +
113B ILE 3.3 0.2 - - - -
114B CYS* 3.9 0.9 - - - -
115B TYR* 2.9 34.9 + - - +
208B PHE* 3.9 23.8 - - - -
2218B GTD 4.0 14.8 + - - -
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 2.7 34.8 + - + +
109B GLN* 3.5 35.9 - - + +
110B LEU 3.1 0.6 - - - -
111B GLY* 1.3 76.4 - - - +
113B ILE* 1.3 64.3 + - + +
115B TYR* 3.7 2.4 + - - +
116B ASN* 3.3 22.5 + - - +
2218B GTD 4.8 8.1 - - - +
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN 3.9 11.0 - - - +
110B LEU* 3.2 11.1 + - + +
112B MET* 1.3 77.7 - - + +
114B CYS* 1.3 64.6 + - - +
115B TYR 3.0 5.2 - - - -
116B ASN* 3.0 28.0 + - - +
119B PHE* 3.2 34.6 - - + +
122B LEU* 4.4 24.9 - - + -
123B LYS* 4.5 13.7 - - - +
126B TYR* 3.7 44.0 - - + -
169B PHE* 4.6 5.2 - - + -
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Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.1 33.7 + - - +
111B GLY 4.0 2.0 - - - +
113B ILE* 1.3 79.1 - - - +
115B TYR* 1.3 58.5 + - - +
116B ASN 3.5 0.2 - - - -
119B PHE* 3.8 22.4 - - - -
169B PHE* 3.9 1.8 - - - -
208B PHE* 3.6 28.5 - - + -
212B ALA* 3.4 4.9 - - - +
213B VAL* 2.8 26.9 + - - -
214B TRP* 3.4 33.8 + - + +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLY* 2.9 28.6 + - - +
112B MET* 4.1 3.4 - - - +
113B ILE 3.0 0.6 - - - -
114B CYS* 1.3 80.0 - - - +
116B ASN* 1.3 62.4 + - - +
117B PRO* 3.4 8.7 - - - +
208B PHE* 3.4 26.8 - + + +
209B SER* 3.0 36.2 + - - -
211B MET* 4.1 34.7 - - + +
212B ALA* 4.1 12.8 - - + +
213B VAL* 4.8 4.1 - - - +
2218B GTD 2.9 55.6 + - - +
----------------------------------------------------------
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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