Contacts of the helix formed by residues 83 - 111 (chain X) 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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X PHE* 4.1 12.8 - - + -
35X TRP* 4.1 13.8 - - + -
37X LEU* 4.0 17.0 - - + -
40X LEU* 4.2 7.2 - - + -
82X ASP* 1.3 73.0 - - - +
84X GLU* 1.3 63.9 + - - +
86X MET* 3.3 9.1 + - - +
87X LEU* 3.0 30.4 + - + +
141X ILE* 4.6 3.6 - - + -
146X LEU* 5.0 7.9 - - + -
149X TYR* 4.1 25.8 - - + -
150X LEU* 3.9 25.1 - - + -
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Residues in contact with GLU 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82X ASP* 3.3 8.3 + - - +
83X VAL* 1.3 77.9 - - - +
85X GLU* 1.3 56.6 + - - +
87X LEU* 3.3 3.1 + - - +
88X ARG* 2.9 65.0 + - - +
138X LEU* 4.0 11.2 - - + -
141X ILE* 4.2 28.0 - - + +
142X GLN* 3.2 20.1 + - - +
146X LEU* 5.5 5.4 - - + +
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Residues in contact with GLU 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ASN* 5.5 2.4 - - - +
80X GLY* 3.6 13.3 - - - -
81X GLU* 3.1 36.8 + - - +
82X ASP* 2.9 26.5 + - - +
84X GLU* 1.3 75.8 - - - +
86X MET* 1.3 62.6 + - - +
88X ARG* 3.4 8.6 + - - +
89X SER* 3.0 27.7 + - - +
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Residues in contact with MET 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28X HIS* 3.3 42.2 + - + +
31X MET* 3.6 37.7 - - + -
32X PHE* 3.7 26.9 - - + -
35X TRP* 3.4 28.7 - - + -
79X ILE 3.3 20.0 - - - +
80X GLY 4.0 8.3 - - - -
82X ASP* 2.9 23.2 + - - +
83X VAL 3.6 3.4 - - - +
85X GLU* 1.3 76.0 - - - +
87X LEU* 1.3 62.2 + - - +
89X SER* 3.3 1.1 + - - -
90X ASP* 3.2 18.5 + - - -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X PHE* 3.7 30.5 - - + -
40X LEU* 5.0 3.8 - - + -
44X GLU* 4.4 8.7 - - - +
83X VAL* 3.0 24.2 + - + +
86X MET* 1.3 73.8 - - - +
88X ARG* 1.3 56.2 + - - +
90X ASP* 3.4 5.3 + - - +
91X LEU* 3.0 27.2 + - - +
133X TRP* 4.8 7.6 - - + -
134X LEU* 3.8 23.8 - - + +
137X GLU* 4.2 13.7 - - + -
138X LEU* 3.8 17.4 - - + +
141X ILE* 4.1 18.6 - - + -
149X TYR* 3.8 22.0 - - - +
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Residues in contact with ARG 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X GLU* 2.9 54.6 + - - +
85X GLU* 3.9 6.7 - - - +
86X MET 3.4 0.2 - - - -
87X LEU* 1.3 69.8 - - - +
89X SER* 1.3 64.6 + - - +
91X LEU* 3.2 6.9 + - + +
92X ALA* 2.9 24.9 + - - +
138X LEU* 3.9 30.0 - - + +
142X GLN* 3.4 18.8 + - - +
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Residues in contact with SER 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24X GLN* 3.4 9.4 + - - +
28X HIS* 4.6 0.9 - - - -
78X ASN* 3.0 51.7 + - - +
79X ILE 4.3 3.6 + - - -
80X GLY* 4.6 1.0 + - - -
85X GLU* 3.0 21.8 + - - +
86X MET 3.3 5.7 + - - -
88X ARG* 1.3 70.7 - - - +
90X ASP* 1.3 58.6 + - - +
92X ALA* 3.4 6.0 + - - +
93X LEU* 2.9 29.6 + - - +
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Residues in contact with ASP 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24X GLN* 3.0 24.0 - - - +
25X TYR* 4.0 18.1 - - + -
28X HIS* 3.0 22.8 + - - -
44X GLU* 2.8 33.0 - - - +
86X MET 3.2 5.9 + - - +
87X LEU* 3.5 8.3 - - - +
89X SER* 1.3 75.9 - - - +
91X LEU* 1.3 65.8 + - - +
93X LEU* 3.2 6.6 + - - +
94X GLU* 3.0 26.3 + - - +
134X LEU* 3.9 18.9 - - + +
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Residues in contact with LEU 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X LEU 3.0 14.7 + - - +
88X ARG* 3.7 10.1 - - + +
90X ASP* 1.3 74.4 - - - +
92X ALA* 1.3 58.3 + - - +
94X GLU* 3.3 1.9 + - - +
95X LEU* 3.0 44.6 + - + +
131X ILE* 3.8 36.6 - - + +
134X LEU* 3.8 15.1 - - + +
135X GLU* 4.1 23.3 - - + +
138X LEU* 3.6 24.9 - - + -
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Residues in contact with ALA 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ASN* 6.1 0.9 - - - +
88X ARG 2.9 16.3 + - - +
89X SER* 3.6 7.6 - - - +
91X LEU* 1.3 76.7 - - - +
93X LEU* 1.3 61.5 + - - +
95X LEU* 3.4 10.2 + - - +
96X ASP* 3.1 29.1 + - - +
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Residues in contact with LEU 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X ASN* 4.9 13.7 - - + +
20X VAL* 3.7 28.0 - - + -
21X ALA* 4.0 21.5 - - + -
24X GLN* 3.6 35.2 - - + +
25X TYR* 5.9 3.6 - - + -
89X SER 2.9 14.9 + - - +
90X ASP* 3.6 9.6 - - - +
92X ALA* 1.3 70.5 - - - +
94X GLU* 1.3 66.8 + - + +
96X ASP* 3.3 8.6 + - + +
97X GLY* 3.0 19.2 + - - -
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Residues in contact with GLU 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X ALA* 4.9 3.8 - - - +
25X TYR* 3.0 27.0 + - + +
51X GLU* 3.2 5.0 - - - +
90X ASP 3.0 18.7 + - - +
91X LEU* 3.6 6.5 - - - +
93X LEU* 1.3 76.0 - - + +
95X LEU* 1.3 57.8 + - - +
97X GLY* 3.2 2.4 + - - -
98X ALA* 2.9 30.7 + - - +
127X GLU* 2.8 19.9 - - - +
130X HIS* 3.2 13.0 - - + +
131X ILE* 3.6 20.7 - - + +
134X LEU* 4.1 10.1 - - + -
201X MN 2.4 36.0 + - - -
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Residues in contact with LEU 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1N MET* 4.7 13.9 - - + -
91X LEU* 3.0 38.6 + - + +
92X ALA* 3.6 8.5 - - - +
94X GLU* 1.3 76.6 - - - +
96X ASP* 1.3 61.0 + - - +
98X ALA* 3.5 5.3 + - + +
99X LYS* 3.1 21.7 + - - +
131X ILE* 3.7 35.2 - - + -
135X GLU* 5.5 2.9 - - - +
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Residues in contact with ASP 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X ASN* 6.5 0.2 - - - -
92X ALA* 3.1 18.1 + - - +
93X LEU* 3.6 12.7 - - + +
95X LEU* 1.3 73.9 - - - +
97X GLY* 1.3 65.8 + - - +
99X LYS* 3.3 30.1 + - - +
100X ASN* 2.9 32.0 + - - +
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Residues in contact with GLY 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LEU* 5.2 0.2 - - - +
17X ASN* 4.1 22.0 - - - -
93X LEU* 3.0 14.8 + - - +
94X GLU* 3.7 3.1 - - - -
96X ASP* 1.3 74.4 - - - +
98X ALA* 1.3 57.2 + - - +
100X ASN* 3.1 3.1 + - - +
101X LEU* 2.8 39.8 + - - +
127X GLU* 5.8 3.1 - - - -
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Residues in contact with ALA 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1N MET* 6.0 0.2 - - - -
94X GLU 2.9 17.6 + - - +
95X LEU* 3.8 6.1 - - + +
97X GLY* 1.3 71.7 - - - +
99X LYS* 1.3 57.7 + - - +
101X LEU* 3.2 6.5 + - - +
102X ARG* 2.9 55.5 + - - +
124X LEU* 4.1 18.1 - - + +
127X GLU* 5.2 4.8 - - + +
128X GLU* 5.6 0.4 - - + -
131X ILE* 4.3 17.5 - - + -
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Residues in contact with LYS 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X LEU 3.1 11.3 + - - +
96X ASP* 3.3 30.4 + - - +
98X ALA* 1.3 79.1 - - - +
100X ASN* 1.3 80.4 + - - +
102X ARG* 3.4 17.4 + - - +
103X GLU* 3.4 15.0 + - - +
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Residues in contact with ASN 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13X LYS* 3.3 36.7 + - - +
14X LEU* 3.7 16.0 - - + +
17X ASN* 2.9 30.4 + - - +
96X ASP* 2.9 26.6 + - - +
97X GLY 3.7 3.8 - - - +
99X LYS* 1.3 88.6 + - - +
101X LEU* 1.3 58.6 + - - +
103X GLU* 3.3 8.8 + - - +
104X ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LEU* 4.2 14.6 - - + +
18X GLU* 5.9 1.1 - - - +
58X TYR* 3.7 22.4 - - - +
97X GLY* 2.8 22.5 + - - +
98X ALA* 3.4 8.3 - - - +
100X ASN* 1.3 72.4 - - - +
102X ARG* 1.3 58.2 + - - +
104X ALA* 3.2 3.4 + - - +
105X ILE* 2.8 38.1 + - + +
120X MET* 4.0 33.7 - - + +
123X ILE* 4.6 4.5 - - + -
124X LEU* 3.9 35.4 - - + +
127X GLU* 4.1 17.9 - - + -
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Residues in contact with ARG 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1N MET* 4.6 16.0 - - - +
112N HIS* 3.4 51.1 + - + +
113N ASP* 4.7 11.7 + - - +
114N TYR* 3.9 9.0 - - + +
115N VAL* 5.3 0.8 - - - +
98X ALA* 2.9 43.0 + - - +
99X LYS* 3.7 10.8 - - - +
101X LEU* 1.3 71.3 - - - +
103X GLU* 1.3 62.1 + - - +
105X ILE* 4.6 1.8 - - - +
106X GLY 3.3 17.3 + - - -
124X LEU* 3.8 23.2 - - + +
128X GLU* 2.7 29.9 + - - -
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Residues in contact with GLU 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N HIS* 5.6 1.1 - - - -
10X TYR* 2.8 34.0 + - - +
13X LYS* 3.9 14.1 + - - -
99X LYS* 3.4 10.6 + - - +
100X ASN* 3.3 12.5 + - - +
102X ARG* 1.3 80.8 - - - +
104X ALA* 1.3 62.2 + - - +
106X GLY* 3.4 1.6 + - - -
107X TYR* 3.1 21.0 + - - +
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Residues in contact with ALA 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X TYR* 3.8 31.5 - - + +
14X LEU* 3.7 15.0 - - + -
100X ASN 2.9 19.7 + - - +
101X LEU 3.7 2.0 - - - +
103X GLU* 1.3 71.8 - - - +
105X ILE* 1.3 58.1 + - - +
107X TYR* 3.2 2.6 + - - +
108X ALA* 2.9 30.1 + - - +
120X MET* 3.7 24.4 - - - +
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Residues in contact with ILE 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N TYR* 3.6 30.1 - - + -
101X LEU* 2.8 25.8 + - + +
104X ALA* 1.3 70.9 - - - +
106X GLY* 1.3 63.6 + - - +
108X ALA* 3.3 2.1 + - - +
109X ASP* 3.0 23.8 + - + +
117X ARG* 3.6 22.2 - - + +
120X MET* 3.6 32.1 - - + +
121X ILE* 3.7 33.4 - - + +
124X LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N HIS* 4.7 7.2 - - - -
114N TYR* 3.7 16.9 + - - -
102X ARG 3.3 10.3 + - - -
103X GLU 3.8 3.1 - - - -
105X ILE* 1.3 78.7 - - - +
107X TYR* 1.3 61.1 + - - +
109X ASP* 3.4 6.1 - - - +
110X SER* 3.1 22.9 + - - -
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Residues in contact with TYR 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X ASP* 2.9 31.5 + - - -
6X LYS* 3.3 37.2 - - + +
7X VAL* 3.6 16.4 - - + -
10X TYR* 3.6 33.0 - + + +
103X GLU 3.1 11.8 + - - +
104X ALA 3.2 6.2 + - - +
106X GLY* 1.3 72.4 - - - +
108X ALA* 1.3 68.5 + - - +
110X SER* 2.9 27.6 + - - -
111X VAL* 3.1 28.5 + - + +
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Residues in contact with ALA 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X VAL* 4.1 10.3 - - + -
104X ALA 2.9 11.3 + - - +
105X ILE 3.6 3.8 - - - +
107X TYR* 1.3 73.8 - - - +
109X ASP* 1.3 60.3 + - - +
111X VAL* 3.4 10.6 + - - +
112X HIS 3.2 3.1 + - - -
113X ASP* 2.9 38.5 + - + +
116X SER* 4.7 1.3 - - - -
117X ARG* 3.9 13.2 - - + +
120X MET* 3.6 30.7 - - + -
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Residues in contact with ASP 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109N ASP* 5.4 4.5 - - - +
114N TYR* 5.8 3.3 - - + +
109O ASP* 5.5 2.8 - - - +
117O ARG* 4.9 2.3 + - - -
105X ILE* 3.0 18.4 + - + +
106X GLY* 3.4 9.2 - - - +
108X ALA* 1.3 76.5 - - - +
110X SER* 1.3 60.1 + - - +
112X HIS* 2.9 21.8 + - - -
114X TYR* 4.0 22.9 + - - -
117X ARG* 3.2 41.0 + - - +
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Residues in contact with SER 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106X GLY 3.1 8.5 + - - -
107X TYR* 2.9 30.7 + - - -
109X ASP* 1.3 81.4 + - - +
111X VAL* 1.3 61.0 + - - +
112X HIS* 3.5 16.2 + - - -
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Residues in contact with VAL 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG* 5.4 0.3 + - - -
4X ASP* 3.9 18.6 - - + +
7X VAL* 3.5 29.4 - - + -
107X TYR* 3.1 36.1 + - + +
108X ALA 3.5 11.9 - - - +
110X SER* 1.3 77.6 + - - +
112X HIS* 1.3 69.9 + - - +
113X ASP* 3.3 6.6 + - + +
----------------------------------------------------------
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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