Contacts of the helix formed by residues 83 - 111 (chain Q) 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 Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q PHE* 4.1 6.7 - - + -
35Q TRP* 4.1 14.4 - - + -
37Q LEU* 4.0 17.7 - - + -
40Q LEU* 4.2 13.0 - - + -
82Q ASP* 1.3 72.8 - - - +
84Q GLU* 1.3 63.7 + - - +
86Q MET* 3.3 9.1 + - - +
87Q LEU* 3.0 31.0 + - + +
141Q ILE* 4.6 3.1 - - + -
146Q LEU* 5.0 7.0 - - + -
149Q TYR* 4.1 25.8 - - + -
150Q LEU* 4.0 24.2 - - + -
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Residues in contact with GLU 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q ASP* 3.3 8.5 + - - +
83Q VAL* 1.3 78.4 - - - +
85Q GLU* 1.3 59.0 + - - +
87Q LEU* 3.3 2.8 + - - +
88Q ARG* 2.9 67.1 + - - +
138Q LEU* 3.9 10.7 - - + +
141Q ILE* 4.2 27.4 - - + +
142Q GLN* 3.2 19.7 + - - +
146Q LEU* 5.4 5.8 - - + +
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Residues in contact with GLU 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q ASN* 5.5 1.9 - - - +
80Q GLY* 3.6 13.9 - - - -
81Q GLU* 3.1 37.4 + - - +
82Q ASP* 2.9 28.0 + - - +
84Q GLU* 1.3 74.9 - - - +
86Q MET* 1.3 62.5 + - - +
88Q ARG* 3.4 8.2 + - - +
89Q SER* 3.0 28.2 + - - +
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Residues in contact with MET 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 3.3 40.9 + - + +
31Q MET* 3.6 38.4 - - + -
32Q PHE* 3.7 27.1 - - + -
35Q TRP* 3.5 27.8 - - + -
79Q ILE 3.3 19.5 - - - +
80Q GLY 4.0 8.7 - - - +
82Q ASP* 2.9 24.1 + - - +
83Q VAL 3.6 3.4 - - - +
85Q GLU* 1.3 77.1 - - - +
87Q LEU* 1.3 61.8 + - - +
89Q SER* 3.3 1.3 + - - -
90Q ASP* 3.2 18.4 + - - -
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Residues in contact with LEU 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q PHE* 3.8 29.6 - - + -
40Q LEU* 5.0 3.4 - - + -
44Q GLU* 4.4 8.7 - - - +
83Q VAL* 3.0 23.2 + - + +
86Q MET* 1.3 75.2 - - - +
88Q ARG* 1.3 57.2 + - - +
90Q ASP* 3.3 5.9 + - - +
91Q LEU* 2.9 26.2 + - - +
133Q TRP* 4.8 8.3 - - + -
134Q LEU* 3.8 24.8 - - + +
137Q GLU* 4.2 13.5 - - + -
138Q LEU* 3.8 17.9 - - + +
141Q ILE* 4.1 18.8 - - + -
149Q TYR* 3.8 22.2 - - - +
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Residues in contact with ARG 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q GLU* 2.9 54.4 + - - +
85Q GLU* 3.9 7.2 - - - +
87Q LEU* 1.3 69.0 - - - +
89Q SER* 1.3 63.5 + - - +
91Q LEU* 3.2 7.1 + - + +
92Q ALA* 2.9 24.1 + - - +
138Q LEU* 3.9 29.6 - - + +
142Q GLN* 3.4 18.4 + - - +
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Residues in contact with SER 89 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q GLN* 3.4 8.9 - - - +
28Q HIS* 4.5 0.9 - - - -
78Q ASN* 3.0 51.8 + - - +
79Q ILE 4.3 3.6 + - - -
80Q GLY* 4.7 1.2 + - - -
85Q GLU* 3.0 22.0 + - - +
86Q MET 3.3 6.0 + - - -
88Q ARG* 1.3 70.6 - - - +
90Q ASP* 1.3 59.4 + - - +
92Q ALA* 3.4 6.0 + - - +
93Q LEU* 2.9 29.5 + - - +
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Residues in contact with ASP 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q GLN* 3.0 19.2 - - - +
25Q TYR* 3.9 18.2 - - + -
28Q HIS* 3.0 27.6 + - - -
44Q GLU* 2.7 33.3 - - - +
86Q MET 3.2 6.4 + - - +
87Q LEU* 3.5 7.9 - - - +
88Q ARG 3.2 0.2 - - - -
89Q SER* 1.3 76.4 - - - +
91Q LEU* 1.3 66.5 + - - +
93Q LEU* 3.2 6.9 + - - +
94Q GLU* 3.0 25.6 + - - +
134Q LEU* 3.9 19.4 - - + +
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Residues in contact with LEU 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q LEU 2.9 17.3 + - - +
88Q ARG* 3.7 11.2 - - + +
90Q ASP* 1.3 70.7 - - - +
92Q ALA* 1.3 58.6 + - - +
94Q GLU* 3.2 2.7 + - - +
95Q LEU* 2.9 47.2 + - + +
131Q ILE* 3.8 36.1 - - + +
134Q LEU* 3.8 15.5 - - + +
135Q GLU* 4.1 23.6 - - + +
138Q LEU* 3.7 24.7 - - + -
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Residues in contact with ALA 92 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q ASN* 6.1 1.3 - - - +
88Q ARG 2.9 16.7 + - - +
89Q SER* 3.6 7.6 - - - +
91Q LEU* 1.3 76.1 - - - +
93Q LEU* 1.3 62.0 + - - +
95Q LEU* 3.4 9.8 + - - +
96Q ASP* 3.1 28.9 + - - +
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Residues in contact with LEU 93 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ASN* 4.9 13.7 - - + +
20Q VAL* 3.7 27.1 - - + -
21Q ALA* 4.0 21.1 - - + -
24Q GLN* 3.6 34.5 - - + +
25Q TYR* 5.9 3.1 - - + -
89Q SER 2.9 15.1 + - - +
90Q ASP* 3.2 10.3 + - - +
92Q ALA* 1.3 71.4 - - - +
94Q GLU* 1.3 68.1 + - + +
96Q ASP* 3.3 8.6 + - + +
97Q GLY* 3.0 19.9 + - - +
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Residues in contact with GLU 94 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ALA* 4.9 3.8 - - - +
25Q TYR* 3.0 26.5 + - + +
51Q GLU* 3.2 4.9 - - - +
90Q ASP 3.0 17.8 + - - +
91Q LEU* 3.6 7.2 - - - +
93Q LEU* 1.3 76.6 - - + +
95Q LEU* 1.3 58.6 + - - +
97Q GLY* 3.2 3.4 + - - -
98Q ALA* 2.9 31.2 + - - +
127Q GLU* 2.8 20.8 - - + +
130Q HIS* 3.2 13.1 - - + +
131Q ILE* 3.6 19.9 - - + +
134Q LEU* 4.1 10.1 - - + -
201Q MN 2.2 35.5 + - - -
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Residues in contact with LEU 95 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 4.7 13.5 - - + -
91Q LEU* 2.9 39.0 + - + +
92Q ALA* 3.6 7.4 - - - +
93Q LEU 3.3 0.2 - - - -
94Q GLU* 1.3 75.4 - - - +
96Q ASP* 1.3 60.4 + - - +
98Q ALA* 3.5 5.9 + - + +
99Q LYS* 3.1 21.7 + - - +
131Q ILE* 3.7 35.2 - - + -
135Q GLU* 5.5 2.2 - - - +
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Residues in contact with ASP 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ASN* 6.5 0.2 - - - -
92Q ALA* 3.1 19.2 + - - +
93Q LEU* 3.3 12.5 + - + +
95Q LEU* 1.3 72.7 - - - +
97Q GLY* 1.3 64.6 + - - +
99Q LYS* 3.2 30.9 + - - +
100Q ASN* 2.9 31.2 + - - +
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Residues in contact with GLY 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q LEU* 5.2 0.2 - - - +
17Q ASN* 4.1 22.1 - - - +
93Q LEU* 3.0 14.4 + - - +
94Q GLU* 3.2 3.3 + - - -
96Q ASP* 1.3 75.1 - - - +
98Q ALA* 1.3 57.7 + - - +
100Q ASN* 3.2 3.4 + - - +
101Q LEU* 2.8 38.2 + - - +
127Q GLU* 5.8 2.9 - - - -
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Residues in contact with ALA 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 6.1 0.4 - - - -
94Q GLU 2.9 17.6 + - - +
95Q LEU* 3.7 6.5 - - + +
97Q GLY* 1.3 72.2 - - - +
99Q LYS* 1.3 57.4 + - - +
101Q LEU* 3.2 6.1 + - - +
102Q ARG* 2.9 55.1 + - - +
124Q LEU* 4.1 17.4 - - + +
127Q GLU* 5.2 4.7 - - + +
131Q ILE* 4.3 17.3 - - + -
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Residues in contact with LYS 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q LEU 3.1 11.0 + - - +
96Q ASP* 3.3 31.2 + - - +
98Q ALA* 1.3 78.0 - - - +
100Q ASN* 1.3 80.3 + - - +
102Q ARG* 3.3 17.4 + - - +
103Q GLU* 3.4 15.7 + - - +
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Residues in contact with ASN 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q LYS* 3.4 36.0 + - - +
14Q LEU* 3.7 16.7 - - + +
17Q ASN* 2.9 30.6 + - - +
96Q ASP* 2.9 26.8 + - - +
97Q GLY 3.8 3.6 - - - +
99Q LYS* 1.3 88.8 + - - +
101Q LEU* 1.3 58.1 + - - +
103Q GLU* 3.3 9.3 + - - +
104Q ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 101 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q LEU* 4.1 15.7 - - + +
18Q GLU* 5.9 1.1 - - - +
58Q TYR* 3.7 22.0 - - - +
97Q GLY 2.8 24.3 + - - +
98Q ALA* 3.4 6.1 - - - +
100Q ASN* 1.3 72.6 - - - +
102Q ARG* 1.3 58.4 + - - +
104Q ALA* 3.2 2.6 + - - +
105Q ILE* 2.8 38.3 + - + +
120Q MET* 3.9 34.3 - - + +
123Q ILE* 4.6 4.3 - - + -
124Q LEU* 3.9 35.4 - - + +
127Q GLU* 4.1 18.6 - - + -
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Residues in contact with ARG 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 4.8 14.4 - - - +
111I VAL 5.6 0.2 + - - -
112I HIS* 3.3 54.0 + - + +
113I ASP* 4.6 10.3 + - - +
114I TYR* 3.9 9.8 - - + +
115I VAL 5.3 1.0 - - - +
98Q ALA* 2.9 42.8 + - - +
99Q LYS* 3.3 11.0 + - - +
101Q LEU* 1.3 71.1 - - - +
103Q GLU* 1.3 61.1 + - - +
105Q ILE* 3.6 1.7 + - - -
106Q GLY 3.3 17.0 + - - -
124Q LEU* 3.8 23.2 - - + +
128Q GLU* 2.7 29.7 + - - -
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Residues in contact with GLU 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I HIS* 5.7 1.1 - - - -
10Q TYR* 2.8 34.1 + - - +
13Q LYS* 3.8 14.8 + - - -
99Q LYS* 3.4 10.5 + - - +
100Q ASN* 3.3 12.7 + - - +
101Q LEU 3.2 0.4 - - - -
102Q ARG* 1.3 77.6 - - - +
104Q ALA* 1.3 64.2 + - - +
106Q GLY* 3.4 1.6 + - - -
107Q TYR* 3.1 21.0 + - - +
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Residues in contact with ALA 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q TYR* 3.9 32.0 - - + +
14Q LEU* 3.7 16.2 - - + -
100Q ASN 2.9 19.0 + - - +
101Q LEU 3.7 2.2 - - - +
103Q GLU* 1.3 72.2 - - - +
105Q ILE* 1.3 57.1 + - - +
107Q TYR* 3.2 2.6 + - - +
108Q ALA* 2.9 30.5 + - - +
120Q MET* 3.7 23.8 - - + +
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Residues in contact with ILE 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR* 3.7 28.0 - - + -
101Q LEU* 2.8 27.6 + - + +
104Q ALA* 1.3 70.0 - - - +
106Q GLY* 1.3 64.1 + - - +
108Q ALA* 3.3 2.4 + - - +
109Q ASP* 3.0 24.8 + - + +
117Q ARG* 3.6 22.2 - - + +
120Q MET* 3.6 32.5 - - + +
121Q ILE* 3.7 34.5 - - + +
124Q LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 106 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I HIS* 4.9 6.3 - - - -
114I TYR* 3.9 15.8 + - - -
102Q ARG 3.3 10.6 + - - -
103Q GLU 3.8 2.7 - - - -
105Q ILE* 1.3 78.0 - - - +
107Q TYR* 1.3 61.3 + - - +
109Q ASP* 3.4 8.1 - - - +
110Q SER* 3.0 22.3 + - - -
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Residues in contact with TYR 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q ASP* 3.0 31.0 + - - -
6Q LYS* 3.3 37.7 - - + +
7Q VAL* 3.6 17.3 - - + -
10Q TYR* 3.6 33.0 - + + +
103Q GLU 3.1 11.2 + - - +
104Q ALA 3.2 6.2 + - - +
106Q GLY* 1.3 74.4 - - - +
108Q ALA* 1.3 63.9 + - - +
110Q SER* 2.8 28.6 + - - -
111Q VAL* 3.1 28.0 + - + +
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Residues in contact with ALA 108 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL* 4.1 10.3 - - + -
104Q ALA 2.9 11.2 + - - +
105Q ILE 3.7 2.9 - - - +
107Q TYR* 1.3 73.0 - - - +
109Q ASP* 1.3 61.3 + - - +
111Q VAL* 3.4 11.2 + - - +
112Q HIS 3.2 3.6 + - - -
113Q ASP* 2.9 39.7 + - + +
116Q SER* 4.6 1.6 - - - -
117Q ARG* 4.0 12.8 - - + +
120Q MET* 3.6 30.7 - - + -
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Residues in contact with ASP 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I ASP* 5.5 1.6 - - - +
114I TYR* 5.9 2.2 - - + +
109P ASP* 5.4 3.6 - - - +
117P ARG* 4.9 2.1 + - - -
105Q ILE* 3.0 14.6 + - + +
106Q GLY* 3.4 13.0 - - - +
108Q ALA* 1.3 77.0 - - - +
110Q SER* 1.3 59.9 + - - +
112Q HIS* 2.9 21.8 + - - -
114Q TYR* 4.0 22.3 + - - -
117Q ARG* 3.2 39.3 + - - +
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Residues in contact with SER 110 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q GLY 3.0 11.4 + - - -
107Q TYR* 2.8 34.6 + - - -
109Q ASP* 1.3 78.4 + - - +
111Q VAL* 1.3 60.5 + - - +
112Q HIS* 3.4 16.2 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG* 5.4 0.2 + - - -
4Q ASP* 3.9 18.6 - - + +
7Q VAL* 3.5 29.4 - - + -
107Q TYR* 3.4 37.0 - - + +
108Q ALA 3.5 11.4 - - - +
110Q SER* 1.3 77.6 + - - +
112Q HIS* 1.3 69.8 + - - +
113Q 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