Contacts of the helix formed by residues 37 - 62 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 3.0 8.5 - - - +
36B ASP* 1.3 89.8 - - - +
38B ASP* 1.3 64.7 + - + +
40B LYS* 3.3 23.7 - - + +
41B LYS* 3.5 16.0 + - - +
104C ASP* 4.2 24.0 - - + +
106C GLY 5.0 2.4 + - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 3.1 15.0 - - - +
37B PRO* 1.3 80.0 - - - +
39B ALA* 1.3 61.7 + - - +
40B LYS 3.1 3.8 - - - -
41B LYS* 3.2 37.8 + - - +
42B PHE* 3.6 15.6 - - - -
99B LEU 5.2 1.6 - - - +
229B ILE* 3.5 36.0 - - + +
230B PHE* 5.1 2.9 - - + +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 4.2 12.3 - - + -
36B ASP* 2.7 28.2 + - + +
38B ASP* 1.3 69.8 - - - +
40B LYS* 1.3 63.8 + - - +
41B LYS 3.3 0.2 - - - -
42B PHE* 3.6 13.1 + - - +
43B TYR* 3.2 34.5 + - + -
228B ALA* 4.6 5.8 + - + +
231B GLY 4.1 3.1 - - - +
232B GLU* 4.0 25.1 - - - +
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 4.2 18.6 - - + -
35B SER 4.6 6.1 + - - +
36B ASP 2.9 11.1 + - - +
37B PRO* 3.3 16.6 - - + +
38B ASP 3.1 0.2 - - - -
39B ALA* 1.3 75.5 - - - +
41B LYS* 1.3 64.9 + - - +
43B TYR* 3.5 3.9 + - - +
44B ALA* 3.0 24.4 + - - +
104C ASP* 2.8 38.2 + - + +
106C GLY* 4.1 4.7 - - - -
107C THR* 3.5 24.8 - - + +
1001C ARC 3.5 43.6 + - + +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO 3.6 15.5 - - - +
38B ASP* 3.2 24.7 + - - +
40B LYS* 1.3 76.8 - - - +
42B PHE* 1.3 57.1 + - + +
44B ALA* 2.9 4.3 + - - +
45B ILE* 2.8 40.5 + - + +
99B LEU* 3.9 39.0 - - + +
105C GLN* 3.6 38.1 + - + +
106C GLY* 4.1 19.3 - - - +
109C LEU* 6.2 1.1 - - + -
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 3.6 21.7 + - - -
39B ALA* 3.6 6.9 + - - +
40B LYS 3.4 0.4 - - - -
41B LYS* 1.3 80.0 - - + +
43B TYR* 1.3 56.8 + - + +
46B THR* 2.9 35.7 + - - -
96B ASP* 3.3 45.8 - - - +
99B LEU* 3.5 38.1 - - + -
100B LEU* 3.7 14.6 - - + -
223B LEU* 4.2 11.2 - - + -
224B LEU* 4.0 13.0 - - + -
228B ALA* 3.4 46.2 - - + -
229B ILE* 3.5 12.8 - - + -
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE 4.2 10.5 - - - -
30B LYS* 3.3 41.2 + - + -
31B GLY* 3.3 35.4 - - - -
34B VAL* 4.1 20.3 - - + +
39B ALA* 3.2 31.0 + - + +
40B LYS* 3.9 4.5 - - - +
42B PHE* 1.3 75.9 - - + +
44B ALA* 1.3 60.5 + - - +
46B THR* 3.9 0.8 - - - -
47B THR* 2.5 33.3 + - - -
224B LEU* 3.7 37.9 + - + -
232B GLU 4.9 13.2 + - - -
1001C ARC 3.6 16.3 - - + +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS 3.0 12.0 + - - +
41B LYS* 2.9 9.3 + - - +
43B TYR* 1.3 75.4 - - - +
45B ILE* 1.3 68.7 + - - +
47B THR* 3.0 12.6 + - - -
48B LEU* 3.2 18.4 + - - +
106C GLY* 3.4 26.7 - - - +
109C LEU* 4.7 5.8 - - + -
110C ALA* 4.0 13.2 - - + +
1001C ARC 3.9 17.4 - - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 2.8 24.9 + - + +
42B PHE 4.1 0.2 - - - +
44B ALA* 1.3 74.5 - - - +
46B THR* 1.3 57.2 + - - +
47B THR 3.2 4.2 + - - -
48B LEU* 3.3 12.2 + - - +
49B VAL* 3.4 14.9 + - + +
92B LEU* 3.1 42.0 - - + +
95B LEU* 3.5 34.3 - - + -
96B ASP* 3.4 21.5 - - - +
99B LEU* 3.7 23.3 - - + -
109C LEU* 3.5 20.0 - - + -
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.4 11.0 - - + -
42B PHE 2.9 19.6 + - - -
45B ILE* 1.3 72.8 - - - +
47B THR* 1.3 58.1 + - - +
49B VAL* 4.7 6.1 - - + -
50B PRO* 3.1 19.1 - - + +
93B LEU* 5.9 1.3 - - + -
96B ASP* 2.4 28.2 + - - +
216B LYS 5.4 0.9 - - - +
219B PHE* 5.2 3.6 - - + -
220B GLY* 3.5 32.1 - - - -
223B LEU* 3.6 7.3 - - + +
224B LEU* 3.6 22.2 - - + -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.0 12.8 - - + +
27B PHE* 3.5 33.5 + - + +
28B LEU* 3.9 20.9 - - + -
43B TYR* 2.5 23.3 + - - -
44B ALA 3.0 2.9 + - - -
46B THR* 1.3 76.8 - - - +
48B LEU* 1.3 65.1 + - - +
49B VAL 3.3 1.6 - - - -
50B PRO* 3.4 3.5 - - - +
51B ALA* 3.2 21.1 + - - +
224B LEU* 5.2 0.2 - - - +
1001C ARC 3.6 32.6 - - + +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 3.2 14.3 + - - +
45B ILE* 3.9 6.7 - - - +
47B THR* 1.3 77.4 - - - +
49B VAL* 1.3 56.8 + - - +
51B ALA* 3.9 2.7 - - - -
52B ILE* 2.7 46.8 + - + +
92B LEU* 4.1 16.8 - - + -
1001B ARC 5.4 3.4 - - + -
109C LEU* 3.6 39.7 - - + +
110C ALA* 4.6 2.5 - - - -
113C GLY* 3.6 32.1 - - - +
117C ILE* 4.0 15.0 - - + -
1001C ARC 3.5 28.5 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE 3.4 17.4 + - - +
46B THR* 4.6 3.6 - - + +
48B LEU* 1.3 80.5 - - - +
50B PRO* 1.3 69.8 - - + +
52B ILE* 4.8 0.2 - - - -
53B ALA* 3.2 17.8 + - - +
89B THR* 3.4 27.0 + - + +
92B LEU* 3.6 24.7 - - + -
93B LEU* 3.5 31.9 - - + -
216B LYS* 3.4 30.5 - - + -
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.8 20.1 - - - +
23B GLY 4.7 0.9 - - - -
24B THR* 3.0 26.3 + - - +
27B PHE* 4.2 18.4 - - + -
46B THR* 3.1 25.1 - - + +
47B THR 3.4 6.3 - - - +
49B VAL* 1.3 94.8 - - + +
51B ALA* 1.3 55.3 + - - -
53B ALA* 3.2 9.0 + - + +
54B PHE* 2.8 26.3 + - - +
216B LYS* 4.7 12.6 - - + -
217B VAL* 4.8 6.5 - - + +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 3.6 18.8 - - + -
47B THR 3.2 18.8 + - - +
48B LEU* 3.2 10.7 + - + +
50B PRO* 1.3 76.1 - - - +
52B ILE* 1.3 68.6 + - - +
54B PHE* 3.0 23.3 + - - +
55B THR* 3.2 8.5 + - - -
117C ILE* 4.0 18.2 - - + +
1001C ARC 5.0 11.9 - - + -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 2.7 32.7 + - + +
49B VAL 3.9 3.6 - - - +
51B ALA* 1.3 71.5 - - - +
53B ALA* 1.3 63.1 + - - +
55B THR* 3.1 23.8 + - - -
56B MET* 3.1 9.3 + - + +
85B ASP* 4.3 21.3 - - - +
88B PHE* 4.0 19.5 - - + -
89B THR* 4.1 13.5 - - - +
92B LEU* 4.0 23.8 - - + -
1001B ARC 4.2 44.0 - - + -
117C ILE* 4.5 13.9 - - + -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.4 31.9 - - + -
49B VAL 3.2 11.4 + - - +
50B PRO 3.2 9.6 + - - +
51B ALA 3.2 0.2 - - - -
52B ILE* 1.3 77.5 - - - +
54B PHE* 1.3 60.3 + - - +
56B MET 3.7 0.2 - - - -
57B TYR* 2.8 37.7 + - + +
85B ASP* 2.9 23.3 + - - +
216B LYS* 4.0 6.1 - - + -
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Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.5 39.0 - - + +
20B MET* 4.2 15.8 - - - +
21B GLY* 4.1 13.0 - - - -
24B THR* 4.9 0.9 - - - +
50B PRO 2.8 13.1 + - - +
51B ALA* 3.0 14.1 + - - +
53B ALA* 1.3 75.5 - - - +
55B THR* 1.3 69.1 + - - +
57B TYR* 3.4 3.0 + - - +
58B LEU* 3.1 29.4 + - + +
140C ILE* 4.0 36.3 - - + -
1001C ARC 5.9 8.5 - - + -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA 3.2 6.8 + - - -
52B ILE* 3.1 11.6 + - - -
54B PHE* 1.3 89.0 - - - +
56B MET* 1.3 72.3 + - + +
58B LEU* 3.2 11.3 + - - +
59B SER* 3.2 10.2 + - - -
1001B ARC 3.2 32.3 - - + -
117C ILE* 3.5 23.7 - - - +
121C THR* 3.8 16.0 + - - +
124C VAL* 5.6 1.1 - - + -
137C TRP* 3.4 17.5 - - + -
140C ILE* 5.1 3.6 - - - +
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Residues in contact with MET 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.1 14.6 + - + +
54B PHE 3.3 0.2 - - - -
55B THR* 1.3 107.5 - - + +
57B TYR* 1.3 62.9 + - - +
59B SER* 2.6 31.4 + - - +
60B MET* 3.3 15.2 - - + +
80B TRP* 5.5 0.9 - - + -
81B ALA* 3.4 22.9 - - + +
84B ALA* 3.3 31.4 - - - -
85B ASP* 3.6 33.2 - - + +
1001B ARC 3.7 32.5 - - + -
124C VAL* 5.0 2.7 - - + -
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.4 33.8 - - + +
16B GLY* 3.7 20.0 - - - +
17B THR* 3.3 21.2 + - - +
20B MET* 4.5 13.2 - - + -
53B ALA* 2.8 30.3 + - + +
54B PHE* 4.0 1.8 - - - +
56B MET* 1.3 71.9 - - - +
58B LEU* 1.3 56.0 + - - +
60B MET* 3.3 28.9 + - + +
61B LEU* 2.9 29.5 + - - +
82B ARG* 3.8 6.3 + - - -
85B ASP* 4.7 8.7 - - - -
208B PHE 3.6 0.5 + - - -
209B MET* 3.3 34.6 + - + -
212B ASP* 2.7 35.7 + - + -
213B VAL* 6.2 0.2 - - + -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.8 15.4 + - + -
54B PHE* 3.1 22.8 + - + +
55B THR 3.2 10.7 + - - +
57B TYR* 1.3 78.1 - - - +
59B SER* 1.3 57.1 + - - +
61B LEU* 3.3 14.0 + - + +
62B LEU* 2.8 58.5 + - + +
136C VAL* 4.0 15.5 - - + -
137C TRP* 3.7 15.5 - - + -
140C ILE* 3.4 33.2 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR 3.2 8.4 + - - -
56B MET* 2.6 31.5 + - - +
58B LEU* 1.3 79.8 - - - +
60B MET* 1.3 59.9 + - - +
62B LEU* 3.3 1.7 + - - -
63B GLY 2.9 23.7 + - - -
64B TYR* 3.1 26.9 + - - -
65B GLY* 3.6 11.2 - - - -
80B TRP* 6.1 0.2 - - - -
81B ALA* 3.3 18.5 - - - +
124C VAL* 5.2 0.7 - - - -
137C TRP* 3.7 18.8 - - - -
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.9 27.8 - - + +
56B MET* 3.3 18.4 - - + +
57B TYR* 3.3 28.7 + - + +
58B LEU 3.3 0.4 - - - -
59B SER* 1.3 78.8 + - - +
61B LEU* 1.3 64.9 + - - +
63B GLY* 3.0 13.3 + - - -
65B GLY* 4.3 3.8 - - - +
79B TYR* 3.7 44.1 + - + -
81B ALA* 3.6 17.9 - - + -
82B ARG* 3.6 50.3 - - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 5.9 1.9 + - - +
10B TRP* 4.0 39.2 - - + +
13B LEU* 4.1 15.3 - - + +
14B ALA* 4.2 20.9 - - + -
17B THR* 4.4 8.1 - - + +
57B TYR 2.9 18.0 + - - +
58B LEU* 3.7 23.3 - - + +
59B SER 3.3 0.2 - - - -
60B MET* 1.3 78.0 - - - +
62B LEU* 1.3 68.8 + - + +
63B GLY 3.2 0.7 + - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 2.8 54.3 + - + +
59B SER* 4.0 3.6 - - - +
61B LEU* 1.3 88.3 - - + +
63B GLY* 1.3 57.7 + - - +
64B TYR* 3.5 6.9 + - + +
129C LYS* 5.3 2.1 + - - -
130C VAL* 4.9 5.0 - - - +
133C TYR* 3.4 60.0 - - + +
136C VAL* 4.5 9.9 - - + -
137C TRP* 4.0 22.7 - - + +
----------------------------------------------------------
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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