Contacts of the helix formed by residues 37 - 61 (chain C) in PDB entry 1BRR
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 PRO 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASP* 4.2 23.5 - - + +
106A GLY 5.0 1.9 + - - -
35C SER 3.2 7.9 - - - +
36C ASP* 1.3 89.7 - - - +
38C ASP* 1.3 63.6 + - + +
40C LYS* 3.1 25.4 - - + +
41C LYS* 3.4 18.0 + - - +
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 3.2 16.0 + - - +
37C PRO* 1.3 84.8 - - + +
39C ALA* 1.3 59.9 + - - +
40C LYS 3.5 0.3 + - - -
41C LYS* 3.7 25.8 + - - +
42C PHE* 3.1 31.2 - - - -
99C LEU 5.5 1.6 - - - +
229C ILE 3.8 7.8 - - - +
230C PHE* 4.4 11.9 - - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.4 11.0 - - + -
36C ASP* 2.7 23.6 + - + +
38C ASP* 1.3 71.4 - - - +
40C LYS* 1.3 65.9 + - - +
42C PHE* 3.2 12.0 + - - +
43C TYR* 3.1 32.5 + - + -
229C ILE* 3.4 20.6 + - + +
231C GLY* 3.5 17.9 - - - +
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 2.8 35.9 + - + +
106A GLY* 4.2 7.4 - - - -
107A THR* 3.3 28.5 - - + +
1000A ARC 4.0 33.0 - - + +
34C VAL* 4.4 20.2 - - + +
35C SER* 4.5 8.4 + - - +
36C ASP 2.9 11.9 + - - +
37C PRO* 3.1 20.0 - - + +
39C ALA* 1.3 76.7 - - - +
41C LYS* 1.3 63.7 + - - +
43C TYR* 3.1 6.2 + - - +
44C ALA* 2.9 23.4 + - - +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLN* 3.8 37.0 + - + +
106A GLY* 4.0 20.8 - - - +
109A LEU* 5.8 2.0 - - + -
37C PRO 3.5 15.0 - - - +
38C ASP* 3.7 22.0 + - - +
40C LYS* 1.3 76.7 - - - +
42C PHE* 1.3 60.0 + - + +
44C ALA* 3.1 3.9 + - - +
45C ILE* 2.8 37.3 + - + +
99C LEU* 3.9 40.0 - - + +
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 3.1 34.1 - - - -
39C ALA* 3.2 6.9 + - - +
41C LYS* 1.3 81.9 - - + +
43C TYR* 1.3 56.7 + - + +
46C THR* 2.5 35.9 + - - +
96C ASP* 3.5 44.6 - - - +
99C LEU* 3.7 36.6 - - + -
100C LEU* 3.8 17.0 - - + -
223C LEU* 4.4 12.8 - - + -
224C LEU* 3.9 10.3 - - + +
229C ILE* 3.4 38.6 - - + -
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Residues in contact with TYR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A ARC 3.5 18.2 - - + -
27C PHE 4.1 11.2 - - - -
30C LYS* 3.4 30.4 + - + -
31C GLY* 3.6 32.5 - - - -
34C VAL* 4.1 25.9 - - + +
39C ALA* 3.1 26.6 + - + +
40C LYS* 3.6 6.3 - - - +
42C PHE* 1.3 76.6 - - + +
44C ALA* 1.3 58.8 + - - +
45C ILE 3.2 0.2 + - - -
46C THR* 3.3 0.9 + - - -
47C THR* 2.6 39.1 + - - -
224C LEU* 3.5 45.9 + - + -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLY* 3.2 29.4 - - - +
109A LEU* 4.7 5.4 - - + -
110A ALA* 3.7 16.4 - - + +
1000A ARC 3.6 18.1 - - + +
40C LYS 2.9 11.3 + - - +
41C LYS* 3.5 8.1 - - - +
43C TYR* 1.3 78.7 - - - +
45C ILE* 1.3 60.2 + - - +
47C THR* 4.3 1.0 - - - -
48C LEU* 3.5 30.2 + - - +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.3 22.7 - - + -
41C LYS* 2.8 23.1 + - + +
44C ALA* 1.3 71.2 - - - +
46C THR* 1.3 63.5 + - - +
47C THR 3.1 2.5 + - - -
48C LEU* 3.3 13.0 + - - +
49C VAL* 3.4 17.9 + - + +
92C LEU* 3.2 43.7 - - + +
95C LEU* 3.8 24.5 - - + -
96C ASP* 3.4 23.8 - - - +
99C LEU* 3.8 29.2 - - + -
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.5 9.4 - - + -
42C PHE 2.5 23.7 + - - -
43C TYR 4.1 1.6 - - - -
45C ILE* 1.3 75.2 - - - +
47C THR* 1.3 56.6 + - - +
49C VAL* 4.4 6.6 - - + +
50C PRO* 3.1 20.8 - - - +
93C LEU* 6.2 1.3 - - + -
96C ASP* 2.6 24.8 + - - +
216C LYS 5.2 1.6 - - - +
219C PHE* 5.1 2.5 - - + -
220C GLY* 3.3 39.3 - - - +
223C LEU* 3.6 8.3 - - + +
224C LEU* 4.0 16.0 - - + +
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A ARC 3.4 41.8 - - + +
24C THR* 4.0 18.1 - - + +
27C PHE* 3.9 19.9 + - + +
28C LEU* 4.0 21.1 - - + +
43C TYR* 2.6 24.1 + - - -
44C ALA 4.3 0.2 - - - -
46C THR* 1.3 78.2 - - - +
48C LEU* 1.3 61.4 + - - +
49C VAL 3.2 0.7 - - - -
50C PRO* 3.0 18.5 - - - +
51C ALA* 3.2 10.7 + - - +
224C LEU* 5.5 0.3 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.7 21.1 - - + +
110A ALA* 4.2 3.8 - - - -
113A GLY* 3.7 36.8 - - - -
114A ALA 3.8 0.2 - - - +
117A ILE* 3.9 17.9 - - + -
1000A ARC 3.6 30.3 - - + -
1002A ARC 5.0 8.5 - - + -
44C ALA 3.5 19.2 + - - +
45C ILE* 3.3 5.9 + - - +
47C THR* 1.3 78.1 - - - +
49C VAL* 1.3 60.2 + - - +
51C ALA* 4.0 3.1 - - + -
52C ILE* 2.8 44.7 + - + +
92C LEU* 4.6 7.6 - - + -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.4 17.9 - - + +
46C THR* 4.4 4.7 - - + +
48C LEU* 1.3 77.5 - - - +
50C PRO* 1.3 66.1 - - + +
52C ILE* 3.6 2.4 + - - -
53C ALA* 3.1 25.5 + - - +
89C THR* 3.5 27.5 + - + +
92C LEU* 3.9 21.3 - - + -
93C LEU* 3.5 27.8 - - + -
216C LYS* 3.5 33.7 - - + +
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Residues in contact with PRO 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 3.8 19.9 - - - +
23C GLY 4.8 1.3 - - - -
24C THR* 3.0 22.2 + - - +
27C PHE* 4.2 18.8 - - + -
46C THR 3.1 19.1 - - - +
47C THR 3.0 16.6 - - - +
49C VAL* 1.3 89.2 - - + +
51C ALA* 1.3 51.8 + - - -
53C ALA* 3.2 8.1 + - + +
54C PHE* 2.7 35.9 + - - +
216C LYS* 4.8 11.2 - - + -
217C VAL* 4.8 7.4 - - + +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.9 20.8 - - + +
1000A ARC 4.8 13.2 - - + -
24C THR* 3.2 22.8 + - + -
47C THR 3.2 12.3 + - - +
48C LEU* 3.2 12.9 + - + +
50C PRO* 1.3 77.6 - - - +
52C ILE* 1.3 61.7 + - - +
54C PHE* 3.3 16.7 + - - +
55C THR* 3.3 17.0 + - - -
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.5 8.3 - - + -
1002A ARC 4.0 43.5 - - + -
48C LEU* 2.8 28.5 + - + +
49C VAL 3.7 3.4 - - - +
51C ALA* 1.3 70.6 - - - +
53C ALA* 1.3 63.9 + - - +
55C THR* 3.2 9.6 + - - -
56C MET* 3.0 22.9 + - + +
85C ASP* 3.6 30.5 - - - +
88C PHE* 4.3 17.3 - - + -
89C THR* 3.8 7.6 - - - +
92C LEU* 4.0 25.6 - - + -
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 3.6 25.6 - - + -
49C VAL 3.1 15.6 + - - +
50C PRO 3.5 4.9 - - - +
52C ILE* 1.3 78.8 - - - +
54C PHE* 1.3 59.2 + - - +
56C MET 3.7 0.2 - - - -
57C TYR* 2.8 37.2 + - + +
85C ASP* 3.2 22.2 + - - +
216C LYS* 3.9 12.3 - - - -
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 4.1 31.2 - - + -
1000A ARC 6.3 4.0 - - + -
17C THR* 3.6 36.6 - - + -
20C MET* 4.2 12.5 - - + +
21C GLY* 3.7 21.3 - - - +
24C THR* 5.1 0.4 - - - +
50C PRO 2.7 16.9 + - - +
51C ALA* 3.4 12.3 - - - +
52C ILE 3.2 0.4 - - - -
53C ALA* 1.3 72.0 - - - +
55C THR* 1.3 66.2 + - - +
57C TYR* 3.2 3.7 + - - +
58C LEU* 2.9 44.6 + - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.7 17.2 - - - +
121A THR* 3.7 16.1 + - - +
124A VAL* 5.5 1.6 - - + -
137A TRP* 3.4 32.6 - - + -
140A ILE* 4.9 3.8 - - - +
1002A ARC 3.7 11.9 - - + -
51C ALA 3.3 10.3 + - - -
52C ILE* 3.2 10.0 + - - -
54C PHE* 1.3 87.8 - - - +
56C MET* 1.3 80.6 + - + +
58C LEU* 4.6 0.7 - - - -
59C SER* 3.2 20.4 + - - -
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Residues in contact with MET 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.1 1.8 - - + -
137A TRP* 5.9 0.2 - - + -
1002A ARC 3.5 42.0 - - + -
52C ILE* 3.0 14.3 + - + +
55C THR* 1.3 104.1 - - + +
57C TYR* 1.3 60.1 + - - +
59C SER* 3.1 21.5 + - - +
60C MET* 3.2 22.7 - - + +
80C TRP* 5.0 2.5 - - - -
81C ALA* 3.2 37.5 - - - +
84C ALA* 3.7 15.9 - - + -
85C ASP* 3.4 36.1 - - + +
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.7 34.4 - - + +
16C GLY* 3.8 20.4 - - - +
17C THR* 3.7 17.9 + - - -
20C MET* 4.3 15.5 - - + -
53C ALA* 2.8 28.8 + - + +
54C PHE* 3.7 3.6 - - - +
56C MET* 1.3 74.7 - - - +
58C LEU* 1.3 66.1 + - - +
60C MET* 3.2 29.2 + - + +
61C LEU* 3.0 20.6 + - - +
82C ARG* 3.9 5.8 + - - -
85C ASP* 4.6 7.9 - - - -
205C THR* 4.8 1.4 + - + -
208C PHE 3.6 1.0 + - - -
209C MET* 3.3 30.5 + - + +
212C ASP* 2.9 37.2 + - + -
213C VAL* 6.1 0.2 - - + -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 4.2 12.1 - - + -
137A TRP* 3.7 17.5 - - + -
140A ILE* 3.4 33.0 - - + -
17C THR* 3.8 20.1 + - + -
54C PHE* 2.9 27.4 + - + +
55C THR 3.7 3.6 - - - +
57C TYR* 1.3 77.3 - - - +
59C SER* 1.3 51.5 + - - +
61C LEU* 2.9 21.7 + - + +
62C LEU* 2.7 55.3 + - + +
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.3 1.8 - - - -
137A TRP* 3.8 19.9 - - - -
55C THR 3.2 11.2 + - - -
56C MET* 3.1 21.1 + - - -
58C LEU* 1.3 78.2 - - - +
60C MET* 1.3 64.8 + - - +
62C LEU* 3.2 2.2 + - - +
63C GLY 3.1 17.5 + - - -
64C TYR* 3.2 28.0 + - - -
65C GLY* 3.2 10.2 + - - -
80C TRP* 6.3 0.4 - - - -
81C ALA* 3.5 17.8 - - - +
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Residues in contact with MET 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.4 20.9 - - + +
56C MET* 3.2 22.7 - - + +
57C TYR* 3.2 37.8 + - + +
59C SER* 1.3 80.9 + - - +
61C LEU* 1.3 62.2 + - - +
63C GLY* 3.5 8.3 + - - -
65C GLY* 4.4 5.8 - - - +
66C LEU* 5.1 0.4 - - - +
79C TYR* 3.4 43.3 + - + -
81C ALA* 3.7 14.4 - - + -
82C ARG* 3.6 52.3 - - + +
85C ASP* 6.0 0.4 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLY 5.6 1.4 - - - +
10C TRP* 3.5 41.1 - - + +
13C LEU* 4.1 10.6 - - + +
14C ALA* 4.1 17.3 - - + +
17C THR* 4.2 14.6 - - + +
57C TYR 3.0 12.0 + - - +
58C LEU* 2.9 27.9 + - + +
60C MET* 1.3 79.2 - - - +
62C LEU* 1.3 67.3 + - + +
63C GLY 3.1 5.1 + - - -
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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