Contacts of the helix formed by residues 84 - 111 (chain F) in PDB entry 1ZMC
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 ASN 84 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLY* 2.9 22.1 + - - +
77E GLU* 2.7 39.3 + - - +
82F ARG 3.7 0.2 + - - -
83F LEU* 1.3 71.7 - - - +
85F LEU* 1.3 63.3 + - - +
86F ASP* 3.3 12.5 + - - +
87F LYS* 3.0 27.4 + - - +
88F MET* 3.1 18.2 + - - +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LEU* 5.9 0.4 - - + -
83F LEU* 3.6 18.6 + - + +
84F ASN* 1.3 74.0 - - - +
86F ASP* 1.3 61.6 + - - +
88F MET* 3.3 7.8 + - + -
89F MET* 2.8 44.8 + - + +
174F LEU 3.5 22.4 - - - +
175F LYS 3.6 22.2 - - - +
176F LYS* 3.7 15.9 - - - -
177F VAL* 4.3 4.3 - - + +
197F TRP* 3.8 24.9 - - + -
200F LEU* 4.2 15.5 - - + -
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Residues in contact with ASP 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASN* 3.2 8.2 + - - +
85F LEU* 1.3 83.5 - - - +
87F LYS* 1.3 57.8 + - - +
89F MET* 3.2 7.0 + - - +
90F GLU* 2.9 29.5 + - - +
175F LYS 4.8 8.1 - - - +
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ALA 3.4 21.1 - - - +
73E SER* 3.7 30.1 - - - +
75E GLY* 3.6 9.0 - - - +
77E GLU* 5.3 1.3 - - - +
84F ASN* 3.0 28.7 + - - +
86F ASP* 1.3 74.4 - - - +
88F MET* 1.3 66.8 + - - +
90F GLU* 3.2 40.2 + - - +
91F GLN 3.2 17.5 + - - -
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Residues in contact with MET 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ARG* 3.1 32.2 + - - +
75E GLY 4.4 0.2 - - - +
76E ILE* 4.2 7.2 - - + -
56F LEU* 4.2 13.8 - - + +
59F ASN* 3.6 45.6 + - + +
60F SER* 4.3 3.8 - - - -
63F TYR* 4.2 13.2 - - + -
83F LEU* 3.7 19.5 - - + -
84F ASN 3.1 11.2 + - - +
85F LEU* 3.6 12.6 - - + +
86F ASP 3.2 0.2 - - - -
87F LYS* 1.3 77.2 - - - +
89F MET* 1.3 63.2 + - - +
90F GLU 3.3 0.2 + - - -
91F GLN* 3.4 10.7 + - - +
92F LYS* 3.4 9.5 + - - +
200F LEU* 4.0 29.8 - - + -
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Residues in contact with MET 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LEU* 4.0 15.0 - - + -
85F LEU* 2.8 31.3 + - + +
86F ASP* 3.7 7.0 - - - +
88F MET* 1.3 78.1 - - - +
90F GLU* 1.3 56.0 + - - +
92F LYS* 3.2 26.7 + - - +
93F SER* 2.8 32.9 + - - +
172F LEU 3.1 33.7 - - - +
173F SER* 4.1 4.5 - - - -
174F LEU 4.0 13.5 - - - +
197F TRP* 3.9 29.6 - - + -
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ASP 2.9 16.0 + - - +
87F LYS* 3.2 46.7 + - - +
89F MET* 1.3 74.2 - - - +
91F GLN* 1.3 55.8 + - - +
93F SER* 3.1 7.5 + - - -
94F THR* 2.8 48.3 + - - +
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Residues in contact with GLN 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E SER* 3.5 27.3 + - - +
74E ARG* 4.0 20.6 - - + +
396E THR 3.4 19.7 + - - +
398E ALA* 3.7 22.0 - - + +
55F ALA* 3.9 10.6 - - - +
59F ASN* 2.7 31.3 + - - +
87F LYS 3.2 3.7 + - - +
88F MET 3.7 8.1 - - - +
89F MET 3.4 0.2 - - - -
90F GLU* 1.3 78.3 - - - +
92F LYS* 1.3 62.6 + - - +
94F THR* 3.7 6.6 - - - +
95F ALA* 3.1 23.7 + - - +
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Residues in contact with LYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F PRO* 3.6 41.4 - - + +
55F ALA* 4.1 13.1 - - + +
56F LEU* 4.0 22.4 - - + -
88F MET 3.4 6.7 + - - +
89F MET* 3.2 33.5 + - - +
91F GLN* 1.3 86.0 + - - +
93F SER* 1.3 71.6 + - - +
95F ALA* 3.2 4.5 + - - +
96F VAL* 3.1 24.7 + - + +
172F LEU* 2.9 25.0 + - - +
173F SER* 3.4 15.8 + - - -
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Residues in contact with SER 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F MET* 2.8 19.3 + - - +
90F GLU* 3.1 8.2 + - - -
92F LYS* 1.3 88.6 + - - +
94F THR* 1.3 58.2 - - - +
96F VAL* 3.4 6.0 + - - +
97F LYS* 2.9 30.3 + - - +
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Residues in contact with THR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E LYS* 6.5 0.9 - - - -
90F GLU* 2.8 32.3 + - - +
91F GLN* 3.7 7.4 - - - +
93F SER* 1.3 76.3 - - - +
95F ALA* 1.3 65.2 + - - +
97F LYS* 3.4 7.1 + - - +
98F ALA* 3.1 24.3 + - + +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E LYS* 3.7 30.5 - - - +
396E THR* 4.1 15.5 - - + +
51F ILE* 4.9 5.6 - - + -
55F ALA* 5.2 0.7 - - + -
91F GLN* 3.1 20.1 + - - +
92F LYS* 3.2 10.5 + - - +
94F THR* 1.3 78.4 - - - +
96F VAL* 1.3 60.6 + - - +
98F ALA* 3.4 3.7 + - - +
99F LEU* 3.2 30.7 + - + +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LEU* 3.3 35.0 - - + +
47F ASN* 4.2 13.5 - - - +
51F ILE* 3.9 13.2 - - + -
52F PRO* 3.9 20.2 - - + -
92F LYS* 3.1 18.2 + - + +
93F SER* 3.8 7.2 - - - +
95F ALA* 1.3 75.0 - - - +
97F LYS* 1.3 64.1 + - - +
99F LEU* 3.3 2.4 + - - +
100F THR* 3.0 36.9 + - + +
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Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F SER 2.9 19.0 + - - +
94F THR* 3.8 7.2 - - - +
95F ALA 3.3 0.4 - - - -
96F VAL* 1.3 79.5 - - - +
98F ALA* 1.3 57.6 + - - +
100F THR* 3.0 9.2 + - - +
101F GLY* 2.9 25.8 + - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E LYS* 3.7 30.1 - - - +
94F THR* 3.1 18.7 + - + +
95F ALA 3.9 1.6 - - - +
97F LYS* 1.3 77.5 - - - +
99F LEU* 1.3 60.3 + - - +
101F GLY* 3.4 2.3 + - - -
102F GLY* 2.9 22.7 + - - -
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E ALA 5.4 4.0 - - - +
390E ALA* 5.2 6.3 - - - +
391E ASN 4.9 2.5 - - - +
392E SER* 4.5 27.1 - - - +
395E LYS* 3.9 33.4 - - + -
396E THR* 4.5 1.3 - - - +
46F LEU* 3.5 21.9 - - + +
51F ILE* 3.8 28.7 - - + -
95F ALA 3.2 17.4 + - - +
96F VAL 3.3 0.4 + - - -
98F ALA* 1.3 73.7 - - - +
100F THR* 1.3 64.8 + - - +
101F GLY 3.0 1.1 - - - -
102F GLY* 3.1 11.3 + - - +
103F ILE* 3.2 19.4 + - - +
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Residues in contact with THR 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F THR* 3.9 20.9 - - + +
41F LEU* 3.6 16.7 + - - +
46F LEU* 3.5 22.9 - - + -
47F ASN* 3.5 25.1 - - - +
96F VAL* 3.0 18.1 + - + +
97F LYS* 3.0 15.6 + - - +
99F LEU* 1.3 72.0 - - - +
101F GLY* 1.3 71.0 + - - +
103F ILE* 3.5 4.3 + - - +
104F ALA* 3.4 18.9 + - - +
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Residues in contact with GLY 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LYS 2.9 15.1 + - - -
98F ALA* 3.4 5.1 + - - -
100F THR* 1.3 82.3 + - - +
102F GLY* 1.3 61.3 + - - +
104F ALA* 3.2 12.9 + - - +
105F HIS* 3.2 24.5 + - - -
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Residues in contact with GLY 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ALA 2.9 15.7 + - - -
99F LEU* 3.1 5.9 + - - -
101F GLY* 1.3 75.5 - - - +
103F ILE* 1.3 56.3 + - - +
105F HIS* 3.1 8.0 + - - +
106F LEU* 2.8 39.6 + - - +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.7 50.7 - - + +
41F LEU* 3.8 22.2 - - + +
42F GLY* 3.5 21.3 - - - +
46F LEU* 3.5 27.1 - - + -
99F LEU 3.2 12.3 + - - +
100F THR 4.0 5.4 - - - +
101F GLY 3.3 0.4 - - - -
102F GLY* 1.3 75.5 - - - +
104F ALA* 1.3 58.2 + - - +
106F LEU* 3.1 10.1 + - + +
107F PHE* 2.8 38.1 + - + +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 3.8 20.1 - - + +
100F THR 3.4 9.4 + - - +
101F GLY* 3.2 12.6 + - - +
103F ILE* 1.3 79.2 - - - +
105F HIS* 1.3 65.1 + - + +
107F PHE* 3.5 5.2 + - - +
108F LYS* 3.3 27.8 + - - +
114F HIS* 6.0 1.1 - - - +
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLY* 3.2 23.7 + - - +
102F GLY* 3.1 11.9 + - - +
104F ALA* 1.3 79.4 - - + +
106F LEU* 1.3 65.5 + - + +
108F LYS* 3.1 10.9 + - + +
109F GLN* 2.9 25.6 + - - +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E ILE 3.9 8.3 - - - +
473E ASN* 3.4 54.5 - - - +
474E PHE* 3.7 13.7 - - - +
19F TYR* 4.9 2.2 - - + -
23F ILE* 3.9 16.8 - - + -
102F GLY* 2.8 28.3 + - - +
103F ILE* 3.6 9.4 - - + +
105F HIS* 1.3 71.6 - - + +
107F PHE* 1.3 66.0 + - - +
109F GLN* 3.3 18.4 + - - +
110F ASN* 2.9 32.8 + - - +
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Residues in contact with PHE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER* 4.7 0.7 - - - -
19F TYR* 3.6 47.3 - - + -
22F ALA* 4.0 6.1 - - + -
23F ILE* 3.9 16.4 - - + -
34F CYS* 3.8 33.0 - - + -
41F LEU* 3.9 31.9 - - + -
103F ILE* 2.8 22.5 + - + +
104F ALA* 3.6 6.5 - - - +
105F HIS 3.2 0.2 - - - -
106F LEU* 1.3 76.7 - - - +
108F LYS* 1.3 62.5 + - + +
110F ASN 3.2 1.7 + - - -
111F LYS 3.0 3.8 + - - -
112F VAL* 2.8 53.0 + - + +
114F HIS* 4.2 16.2 - - + -
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ALA* 3.3 15.1 + - - +
105F HIS* 3.1 13.8 + - + +
107F PHE* 1.3 79.3 - - + +
109F GLN* 1.3 62.7 + - - +
111F LYS* 3.1 16.0 + - - +
112F VAL 5.0 4.0 - - - +
114F HIS* 6.6 0.2 - - - -
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Residues in contact with GLN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474E PHE* 3.0 33.7 + - - +
27F GLN* 6.1 0.4 - - - +
105F HIS 2.9 16.3 + - - +
106F LEU* 3.5 20.0 - - - +
108F LYS* 1.3 77.8 - - - +
110F ASN* 1.3 70.2 + - - +
111F LYS* 3.7 3.5 + - - +
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E LYS* 4.8 7.4 + - - +
472E ILE 4.9 0.6 + - - -
23F ILE* 3.7 26.7 - - + +
26F ALA* 3.2 31.6 - - + +
27F GLN* 3.5 26.5 + - - +
106F LEU* 2.9 33.3 + - - +
107F PHE 4.1 2.2 - - - +
108F LYS 3.1 0.2 - - - -
109F GLN* 1.3 96.1 + - - +
111F LYS* 1.3 69.5 + - - +
112F VAL* 3.2 7.2 - - + -
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Residues in contact with LYS 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ALA* 5.0 2.2 - - + +
31F LYS* 6.0 2.8 - - - +
32F THR 4.1 8.0 + - - +
107F PHE 3.0 4.5 + - - -
108F LYS* 3.1 12.7 + - - +
109F GLN 4.9 3.4 - - - +
110F ASN* 1.3 80.6 - - - +
112F VAL* 1.3 64.7 + - - +
113F VAL* 3.4 10.6 + - - +
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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