Contacts of the helix formed by residues 83 - 111 (chain O) in PDB entry 1BFR
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 83 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O PHE* 4.1 6.5 - - + -
35O TRP* 4.1 14.3 - - + -
37O LEU* 4.0 17.9 - - + -
40O LEU* 4.2 13.7 - - + -
82O ASP* 1.3 74.1 - - - +
84O GLU* 1.3 63.7 + - - +
86O MET* 3.3 9.2 + - - +
87O LEU* 3.0 30.8 + - + +
141O ILE* 4.6 3.6 - - + -
146O LEU* 5.0 6.7 - - + -
149O TYR* 4.1 25.8 - - + -
150O LEU* 4.0 24.5 - - + -
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Residues in contact with GLU 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O ASP* 3.3 8.5 + - - +
83O VAL* 1.3 78.6 - - - +
85O GLU* 1.3 58.2 + - - +
87O LEU* 3.3 2.8 + - - +
88O ARG* 2.9 65.7 + - - +
138O LEU* 4.0 10.8 - - + -
141O ILE* 4.2 27.8 - - + +
142O GLN* 3.2 20.3 + - - +
146O LEU* 5.4 6.0 - - + +
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Residues in contact with GLU 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ASN* 5.5 2.3 - - - +
80O GLY* 3.6 13.4 - - - -
81O GLU* 3.1 37.1 + - - +
82O ASP* 2.9 26.9 + - - +
84O GLU* 1.3 75.7 - - - +
86O MET* 1.3 62.6 + - - +
88O ARG* 3.4 8.9 + - + +
89O SER* 3.0 28.4 + - - +
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Residues in contact with MET 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O HIS* 3.3 40.6 + - + +
31O MET* 3.6 38.8 - - + -
32O PHE* 3.7 26.7 - - + -
35O TRP* 3.5 28.5 - - + -
79O ILE 3.3 20.2 - - - +
80O GLY 4.0 7.6 - - - -
82O ASP* 2.9 24.6 + - - +
83O VAL 3.6 3.4 - - - +
85O GLU* 1.3 75.1 - - - +
87O LEU* 1.3 62.6 + - - +
89O SER* 3.3 0.9 + - - -
90O ASP* 3.2 18.2 + - - -
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Residues in contact with LEU 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O PHE* 3.8 29.8 - - + -
40O LEU* 5.0 2.5 - - + -
44O GLU* 4.4 9.6 - - - +
83O VAL* 3.0 23.4 + - + +
86O MET* 1.3 74.2 - - - +
88O ARG* 1.3 57.4 + - - +
90O ASP* 3.3 5.3 + - - +
91O LEU* 2.9 26.7 + - - +
133O TRP* 4.8 7.4 - - + -
134O LEU* 3.8 25.5 - - + +
137O GLU* 4.2 12.8 - - + -
138O LEU* 3.8 19.2 - - + +
141O ILE* 4.1 18.6 - - + -
149O TYR* 3.8 23.1 - - - +
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Residues in contact with ARG 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O GLU* 2.9 56.0 + - - +
85O GLU* 3.9 7.2 - - - +
86O MET 3.4 0.2 - - - -
87O LEU* 1.3 69.3 - - - +
89O SER* 1.3 64.3 + - - +
91O LEU* 3.2 6.7 + - + +
92O ALA* 2.9 24.5 + - - +
138O LEU* 3.9 30.9 - - + +
142O GLN* 3.4 17.8 + - - +
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Residues in contact with SER 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O GLN* 3.4 10.2 - - - +
28O HIS* 4.5 0.9 - - - -
78O ASN* 3.0 50.2 + - - +
79O ILE 4.3 4.5 + - - -
80O GLY* 4.7 1.2 + - - -
85O GLU* 3.0 20.5 + - - +
86O MET 3.3 6.2 + - - -
88O ARG* 1.3 70.3 - - - +
90O ASP* 1.3 58.7 + - - +
92O ALA* 3.4 5.6 + - - +
93O LEU* 2.9 29.5 + - - +
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Residues in contact with ASP 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O GLN* 3.0 19.6 - - - +
25O TYR* 3.9 18.6 - - + -
28O HIS* 3.0 26.7 + - - -
44O GLU* 2.7 32.7 - - - +
86O MET 3.2 6.6 + - - +
87O LEU* 3.5 9.1 - - - +
89O SER* 1.3 76.6 - - - +
91O LEU* 1.3 66.3 + - - +
93O LEU* 3.2 6.7 + - - +
94O GLU* 3.0 26.7 + - - +
134O LEU* 3.9 18.3 - - + +
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Residues in contact with LEU 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O LEU 2.9 17.6 + - - +
88O ARG* 3.7 11.9 - - + +
90O ASP* 1.3 69.4 - - - +
92O ALA* 1.3 57.7 + - - +
94O GLU* 3.2 2.6 + - - +
95O LEU* 2.9 46.8 + - + +
131O ILE* 3.8 37.2 - - + +
134O LEU* 3.8 15.8 - - + +
135O GLU* 4.1 24.0 - - + +
138O LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ASN* 6.1 1.1 - - - +
88O ARG 2.9 17.6 + - - +
89O SER* 3.6 7.2 - - - +
91O LEU* 1.3 76.6 - - - +
93O LEU* 1.3 62.3 + - - +
95O LEU* 3.4 10.2 + - - +
96O ASP* 3.1 28.9 + - - +
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Residues in contact with LEU 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O ASN* 4.9 14.1 - - + +
20O VAL* 3.7 28.7 - - + -
21O ALA* 4.0 22.2 - - + +
24O GLN* 3.6 34.8 - - + +
25O TYR* 5.9 3.6 - - + -
89O SER 2.9 14.9 + - - +
90O ASP* 3.2 9.6 + - - +
92O ALA* 1.3 71.0 - - - +
94O GLU* 1.3 66.8 + - + +
96O ASP* 3.3 8.3 + - + +
97O GLY* 3.0 20.0 + - - -
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Residues in contact with GLU 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O ALA* 4.9 4.3 - - - +
25O TYR* 3.0 26.2 + - + +
51O GLU* 3.2 4.5 - - - +
90O ASP 3.0 19.0 + - - +
91O LEU* 3.6 7.0 - - - +
93O LEU* 1.3 76.2 - - + +
95O LEU* 1.3 58.2 + - - +
97O GLY* 3.2 2.5 + - - -
98O ALA* 2.9 31.4 + - - +
127O GLU* 2.8 21.1 - - + +
130O HIS* 3.2 12.3 - - + +
131O ILE* 3.6 19.8 - - + +
134O LEU* 4.1 9.9 - - + -
201O MN 2.2 36.9 + - - -
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Residues in contact with LEU 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O LEU* 2.9 38.9 + - + +
92O ALA* 3.6 8.5 - - - +
93O LEU 3.3 0.2 - - - -
94O GLU* 1.3 76.5 - - - +
96O ASP* 1.3 60.4 + - - +
98O ALA* 3.5 5.1 + - + +
99O LYS* 3.1 21.5 + - - +
131O ILE* 3.7 35.2 - - + -
135O GLU* 5.5 1.8 - - - +
1X MET* 4.5 14.4 - - + -
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Residues in contact with ASP 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O ASN* 6.5 0.2 - - - -
92O ALA* 3.1 19.2 + - - +
93O LEU* 3.6 12.3 - - + +
95O LEU* 1.3 73.7 - - - +
97O GLY* 1.3 66.6 + - - +
99O LYS* 3.2 30.3 + - - +
100O ASN* 2.9 31.3 + - - +
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Residues in contact with GLY 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O LEU* 5.2 0.3 - - - +
17O ASN* 4.1 22.6 - - - +
93O LEU* 3.0 15.0 + - - +
94O GLU* 3.2 3.1 + - - -
96O ASP* 1.3 74.5 - - - +
98O ALA* 1.3 57.1 + - - +
100O ASN* 3.2 3.2 + - - +
101O LEU* 2.8 39.4 + - - +
127O GLU* 5.8 3.1 - - - -
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Residues in contact with ALA 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O GLU 2.9 15.6 + - - +
95O LEU* 3.7 7.2 - - + +
97O GLY* 1.3 73.0 - - - +
99O LYS* 1.3 57.6 + - - +
101O LEU* 3.2 6.1 + - - +
102O ARG* 2.9 54.4 + - - +
124O LEU* 4.1 17.9 - - + +
127O GLU* 5.2 5.1 - - + +
131O ILE* 4.3 17.5 - - + -
1X MET* 6.0 0.4 - - - -
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Residues in contact with LYS 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O LEU 3.1 11.3 + - - +
96O ASP* 3.3 31.2 + - - +
98O ALA* 1.3 80.2 - - - +
100O ASN* 1.3 80.5 + - - +
102O ARG* 3.3 17.1 + - - +
103O GLU* 3.4 14.8 + - - +
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Residues in contact with ASN 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O LYS* 3.4 36.2 + - - +
14O LEU* 3.7 17.1 - - + +
17O ASN* 2.9 30.2 + - - +
96O ASP* 2.9 25.9 + - - +
97O GLY 3.8 3.6 - - - +
99O LYS* 1.3 87.4 + - - +
101O LEU* 1.3 58.0 + - - +
103O GLU* 3.3 9.5 + - - +
104O ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O LEU* 4.3 15.3 - - + -
18O GLU* 5.9 1.3 - - - +
58O TYR* 3.7 22.4 - - - +
97O GLY 2.8 24.7 + - - +
98O ALA 3.4 6.3 - - - +
100O ASN* 1.3 71.3 - - - +
102O ARG* 1.3 58.1 + - - +
104O ALA* 3.2 2.7 + - - +
105O ILE* 2.8 38.0 + - + +
120O MET* 3.9 33.9 - - + +
123O ILE* 4.6 4.3 - - + -
124O LEU* 3.9 35.7 - - + +
127O GLU* 4.1 18.2 - - + -
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Residues in contact with ARG 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O ALA* 2.9 44.3 + - - +
99O LYS* 3.3 10.9 + - - +
101O LEU* 1.3 72.4 - - - +
103O GLU* 1.3 61.3 + - - +
105O ILE* 3.6 0.4 + - - -
106O GLY 3.3 16.8 + - - -
124O LEU* 3.8 22.2 - - + +
128O GLU* 2.7 30.3 + - - -
1X MET* 4.7 13.6 - - - +
111X VAL 5.4 0.4 + - - -
112X HIS* 3.1 55.5 + - + +
113X ASP* 4.4 11.5 + - - +
114X TYR* 3.8 10.7 - - + +
115X VAL 5.2 0.4 - - - +
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Residues in contact with GLU 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O TYR* 2.8 34.9 + - - +
13O LYS* 3.8 13.8 + - - -
99O LYS* 3.4 10.6 + - - +
100O ASN* 3.3 12.1 + - - +
102O ARG* 1.3 78.1 - - - +
104O ALA* 1.3 65.2 + - - +
106O GLY* 3.4 1.4 + - - -
107O TYR* 3.1 20.3 + - - +
112X HIS* 5.5 2.0 - - - -
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Residues in contact with ALA 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O TYR* 3.9 31.6 - - + -
14O LEU* 3.7 15.7 - - + -
100O ASN 2.9 19.0 + - - +
101O LEU 3.7 2.0 - - - +
103O GLU* 1.3 72.6 - - - +
105O ILE* 1.3 58.2 + - - +
107O TYR* 3.2 2.6 + - - +
108O ALA* 2.9 30.7 + - - +
120O MET* 3.7 24.0 - - + +
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Residues in contact with ILE 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O LEU* 2.8 26.9 + - + +
102O ARG 4.0 0.2 - - - +
104O ALA* 1.3 70.7 - - - +
106O GLY* 1.3 64.1 + - - +
108O ALA* 3.3 1.9 + - - +
109O ASP* 3.0 25.6 + - + +
117O ARG* 3.6 22.4 - - + +
120O MET* 3.6 30.3 - - + +
121O ILE* 3.7 33.2 - - + +
124O LEU* 3.8 19.1 - - + -
114X TYR* 3.6 38.8 - - + -
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Residues in contact with GLY 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG 3.3 11.0 + - - -
103O GLU 3.8 3.4 - - - -
104O ALA 3.3 0.2 - - - -
105O ILE* 1.3 78.6 - - - +
107O TYR* 1.3 59.7 + - - +
109O ASP* 3.4 7.7 - - - +
110O SER* 3.0 22.2 + - - -
112X HIS* 4.8 6.7 - - - -
114X TYR* 3.8 15.4 + - - -
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Residues in contact with TYR 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O ASP* 3.0 31.4 + - - -
6O LYS* 3.3 37.7 - - + +
7O VAL* 3.6 16.8 - - + -
10O TYR* 3.6 32.3 - + + +
103O GLU 3.1 11.8 + - - +
104O ALA 3.2 6.5 + - - +
106O GLY* 1.3 73.5 - - - +
108O ALA* 1.3 63.8 + - - +
110O SER* 2.8 28.7 + - - -
111O VAL* 3.1 28.6 + - + +
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Residues in contact with ALA 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 4.1 10.8 - - + -
104O ALA 2.9 11.7 + - - +
105O ILE 3.7 3.1 - - - +
107O TYR* 1.3 72.5 - - - +
109O ASP* 1.3 61.2 + - - +
111O VAL* 3.4 10.0 + - - +
112O HIS 3.2 3.5 + - - -
113O ASP* 2.9 39.3 + - + +
116O SER* 4.6 1.6 - - - -
117O ARG* 4.0 12.3 - - + +
120O MET* 3.6 30.7 - - + -
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Residues in contact with ASP 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109N ASP* 5.3 5.1 - - - +
117N ARG* 4.8 2.3 + - - -
105O ILE* 3.0 13.8 + - + +
106O GLY* 3.4 12.6 - - - +
108O ALA* 1.3 76.8 - - - +
110O SER* 1.3 60.0 + - - +
112O HIS* 2.9 22.0 + - - -
114O TYR* 4.0 22.3 + - - -
117O ARG* 3.2 40.0 + - - +
109X ASP* 5.5 3.1 - - - +
114X TYR* 6.2 0.8 - - - -
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Residues in contact with SER 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O GLY 3.0 12.3 + - - -
107O TYR* 2.8 34.8 + - - -
109O ASP* 1.3 78.5 + - - +
111O VAL* 1.3 60.4 + - - +
112O HIS* 3.4 16.3 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N ARG* 5.5 0.3 + - - -
4O ASP* 3.9 18.6 - - + +
7O VAL* 3.5 30.1 - - + -
107O TYR* 3.1 36.5 + - + +
108O ALA 3.5 11.4 - - - +
110O SER* 1.3 77.2 + - - +
112O HIS* 1.3 70.2 + - - +
113O ASP* 3.3 7.3 + - + +
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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