Contacts of the helix formed by residues 38 - 64 (chain M) 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 LYS 38 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M LYS* 5.5 6.7 - - + +
36M GLY* 2.9 17.7 + - - +
37M LEU* 1.3 70.3 - - - +
39M ARG* 1.3 61.6 + - - +
41M ASN* 3.2 8.8 + - - +
42M ASP* 3.0 28.8 + - - +
153M GLN 3.1 5.9 + - - +
154M ILE 3.0 26.1 + - - +
156M GLU* 3.6 32.3 - - - +
39X ARG* 5.3 7.5 - - - +
157X GLU* 3.0 25.9 + - - +
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Residues in contact with ARG 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L LYS* 5.0 9.3 - - - +
154L ILE* 5.9 7.2 - - - +
155L ARG* 3.3 24.4 - - - +
38M LYS* 1.3 70.9 - - - +
40M LEU* 1.3 65.9 + - - +
42M ASP* 3.3 5.3 + - - +
43M VAL* 3.1 37.0 + - + +
133M TRP* 4.0 14.1 - - - +
137M GLU* 3.1 40.0 + - - -
140M LEU* 6.2 0.2 - - - +
152M ALA 4.1 1.8 - - - -
153M GLN* 2.6 55.1 + - - +
155M ARG 3.8 11.8 + - - +
156M GLU* 4.6 7.6 - - - +
157M GLU* 4.2 26.1 - - + +
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Residues in contact with LEU 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M PHE* 3.7 34.5 - - + -
37M LEU* 3.1 16.8 + - + +
39M ARG* 1.3 85.0 - - - +
41M ASN* 1.3 64.8 + - - +
43M VAL* 4.7 1.6 - - - +
44M GLU* 3.1 29.6 + - - +
83M VAL* 4.2 22.0 - - + -
87M LEU* 5.0 3.4 - - + -
133M TRP* 4.1 20.0 - - + -
149M TYR* 3.6 22.2 - - + +
153M GLN* 3.5 39.1 + - + +
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Residues in contact with ASN 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M ALA* 3.1 32.9 - - - +
30M ARG* 2.9 27.5 + - - +
32M PHE* 3.7 1.8 - - - +
33M LYS* 3.4 38.5 - - + +
37M LEU 3.1 8.5 + - - +
38M LYS* 3.4 10.4 + - - +
40M LEU* 1.3 75.7 - - - +
42M ASP* 1.3 77.4 + - - +
45M TYR* 2.9 24.4 + - - +
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Residues in contact with ASP 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M LYS* 3.0 16.4 + - - +
39M ARG* 3.8 5.1 - - - +
41M ASN* 1.3 88.4 + - - +
43M VAL* 1.3 61.0 + - + +
45M TYR* 3.8 3.4 - - - +
46M HIS* 2.7 44.6 + - + +
156M GLU* 3.3 37.7 - - - +
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Residues in contact with VAL 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M ARG* 3.1 29.4 + - + +
40M LEU 4.4 0.7 - - - +
42M ASP* 1.3 75.0 - - + +
44M GLU* 1.3 61.3 + - - +
46M HIS* 3.2 9.2 + - + +
47M GLU* 3.0 30.2 + - + +
133M TRP* 3.5 55.4 - - + +
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Residues in contact with GLU 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 3.5 24.9 - - - +
28M HIS* 3.3 20.1 - - - +
29M ALA* 3.9 19.5 - - + +
32M PHE* 3.8 17.6 - - + -
40M LEU 3.1 19.5 + - - +
43M VAL* 1.3 72.9 - - - +
45M TYR* 1.3 63.4 + - - +
47M GLU* 3.2 7.7 + - - +
48M SER* 2.9 21.8 + - - -
87M LEU* 4.6 2.5 - - - -
90M ASP* 2.7 28.8 - - - +
133M TRP* 3.6 27.2 - - + -
134M LEU* 4.1 3.1 - - - +
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Residues in contact with TYR 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M PHE* 3.6 33.0 - + - -
29M ALA* 3.4 11.4 - - + +
30M ARG* 3.7 28.0 - - - +
41M ASN* 2.9 22.0 + - - +
42M ASP* 3.8 3.4 - - - +
44M GLU* 1.3 74.7 - - - +
46M HIS* 1.3 82.7 + + - +
48M SER* 3.2 8.7 - - - -
49M ILE* 3.0 43.9 + - + +
200N HEM 3.6 29.4 + - + +
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Residues in contact with HIS 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ASP* 2.7 35.2 + - + +
43M VAL* 3.2 9.1 + - + +
45M TYR* 1.3 95.8 - + - +
47M GLU* 1.3 65.9 + - + +
49M ILE* 3.2 11.3 + - + +
50M ASP* 2.9 27.6 + - - +
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Residues in contact with GLU 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 3.2 37.8 + - + -
43M VAL* 3.0 21.2 + - + +
44M GLU* 3.6 14.5 - - - +
46M HIS* 1.3 74.4 - - + +
48M SER* 1.3 62.5 + - - +
50M ASP* 3.1 7.6 + - - +
51M GLU* 3.1 27.9 + - - +
130M HIS* 3.5 43.2 - - + +
133M TRP* 3.8 27.5 - - - +
134M LEU* 4.6 1.4 - - - +
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Residues in contact with SER 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ILE* 3.3 19.7 + - - +
25M TYR* 3.9 8.4 - - - +
26M PHE* 3.4 28.9 - - - -
44M GLU 2.9 12.6 + - - -
45M TYR* 3.2 11.7 - - - -
47M GLU* 1.3 72.9 - - - +
49M ILE* 1.3 63.0 + - - -
51M GLU* 3.1 8.7 + - - +
52M MET* 3.0 41.3 + - - +
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Residues in contact with ILE 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M TYR* 3.0 51.0 + - + +
46M HIS* 3.2 12.5 + - + +
48M SER* 1.3 74.5 - - - +
50M ASP* 1.3 62.5 + - - +
52M MET* 3.2 15.2 - - + +
53M LYS* 2.9 31.8 + - - +
200N HEM 3.8 60.1 - - + +
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Residues in contact with ASP 50 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M HIS* 2.9 22.9 + - - +
47M GLU* 3.1 9.4 + - - +
49M ILE* 1.3 72.4 - - - +
51M GLU* 1.3 59.5 + - - +
53M LYS* 3.4 16.9 + - - +
54M HIS* 2.9 41.3 + - + +
126M ASP* 5.1 7.7 - - - +
130M HIS* 2.8 32.9 + - + -
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Residues in contact with GLU 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLU* 2.8 12.0 - - - +
21M ALA* 3.9 15.9 - - + +
22M ILE* 3.6 24.0 - - + +
25M TYR* 3.6 9.9 - - + -
47M GLU 3.1 14.1 + - - +
48M SER* 3.1 3.6 + - - +
50M ASP* 1.3 71.1 - - - +
52M MET* 1.3 55.9 + - - +
54M HIS* 2.8 14.7 + - - +
55M ALA* 2.8 35.2 + - - +
94M GLU* 3.2 5.9 - - - +
127M GLU* 2.9 2.3 - - - +
130M HIS* 3.4 5.8 + - - -
201M MN 2.1 35.2 + - - -
202M MN 2.0 35.1 + - - -
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Residues in contact with MET 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ILE* 3.5 23.0 - - + +
26M PHE* 4.1 3.8 - - + -
48M SER* 3.0 37.5 + - - +
49M ILE* 3.2 19.3 - - + +
51M GLU* 1.3 74.7 - - - +
53M LYS* 1.3 63.3 + - - +
55M ALA* 3.2 2.9 + - - +
56M ASP* 3.0 20.8 + - - +
200N HEM 2.2 100.9 - - + +
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Residues in contact with LYS 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M ILE* 2.9 24.7 + - - +
50M ASP* 3.6 18.1 + - - +
52M MET* 1.3 75.6 - - - +
54M HIS* 1.3 63.6 + - + +
56M ASP* 3.4 9.2 + - - +
57M ARG* 3.1 27.2 + - - +
200N HEM 3.5 42.2 - - + +
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Residues in contact with HIS 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLU* 3.6 15.5 - - + +
50M ASP* 2.9 29.4 + - + +
51M GLU* 2.8 12.5 + - - +
53M LYS* 1.3 72.4 - - + +
55M ALA* 1.3 63.5 + - - +
57M ARG* 2.9 25.3 + - - +
58M TYR* 3.1 17.9 + - + -
123M ILE* 3.6 29.9 - - + +
126M ASP* 2.8 38.5 + - + -
127M GLU* 3.1 18.2 - - - -
130M HIS* 4.9 0.4 - + - -
202M MN 2.5 24.0 + - - -
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Residues in contact with ALA 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 3.8 22.6 - - + +
18M GLU* 4.2 8.2 - - + +
19M LEU* 4.6 2.9 - - + -
22M ILE* 4.0 13.5 - - + -
51M GLU 2.8 15.8 + - - +
52M MET 3.4 3.8 - - - +
54M HIS* 1.3 69.6 - - - +
56M ASP* 1.3 63.4 + - - +
58M TYR* 3.2 8.2 + - - +
59M ILE* 2.9 27.6 + - - +
200N HEM 3.4 22.4 - - + -
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Residues in contact with ASP 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M MET 3.0 13.3 + - - +
53M LYS* 3.6 12.3 - - - +
55M ALA* 1.3 76.7 - - - +
57M ARG* 1.3 60.9 + - - +
59M ILE* 3.5 2.3 + - - +
60M GLU* 3.0 35.2 + - - +
26N PHE* 3.4 19.5 - - + -
30N ARG* 2.9 45.0 + - - +
200N HEM 3.6 13.2 - - + +
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Residues in contact with ARG 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M LYS* 3.1 15.0 + - - +
54M HIS* 2.9 18.1 + - - +
56M ASP* 1.3 72.4 - - + +
58M TYR* 1.3 62.5 + - - +
60M GLU* 3.5 5.5 + - - +
61M ARG* 3.0 23.6 + - - +
119M MET* 3.7 38.9 - - - +
122M GLU* 3.0 49.0 + - - +
123M ILE* 4.1 19.1 - - + +
126M ASP* 5.8 1.4 + - - -
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Residues in contact with TYR 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LEU* 4.2 20.9 - - + +
14M LEU* 3.8 30.2 - - + +
15M LEU* 4.0 26.0 - - + -
18M GLU* 3.8 27.2 + - + -
54M HIS 3.1 20.2 + - - -
55M ALA* 3.7 4.9 - - - +
57M ARG* 1.3 75.5 - - - +
59M ILE* 1.4 64.3 + - - +
61M ARG* 3.1 5.2 + - - +
62M ILE* 2.9 32.9 + - + +
101M LEU* 3.7 22.7 - - - +
119M MET* 3.5 28.3 - - + -
120M MET* 4.4 3.1 - - + +
123M ILE* 3.6 26.4 - - + +
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Residues in contact with ILE 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 4.0 17.9 - - + -
55M ALA 2.9 24.3 + - - +
56M ASP* 3.8 4.0 - - - +
58M TYR* 1.4 70.1 - - - +
60M GLU* 1.3 63.7 + - - +
62M ILE* 4.7 0.6 - - - +
63M LEU* 3.1 41.8 + - + +
69M PRO* 3.8 19.0 - - + +
71M LEU* 3.8 26.7 - - + -
26N PHE* 3.8 28.5 - - + -
27N LEU* 4.0 8.5 - - + -
30N ARG* 3.9 19.1 - - + -
200N HEM 4.0 9.6 - - + -
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Residues in contact with GLU 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ASP* 3.0 41.1 + - - +
57M ARG* 3.9 5.2 - - - +
59M ILE* 1.3 77.3 - - - +
61M ARG* 1.3 59.9 + - - +
63M LEU* 3.5 6.4 + - + +
64M PHE* 3.1 22.5 + - - +
30N ARG* 3.2 25.2 + - + +
33N LYS* 3.4 30.9 + - - -
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Residues in contact with ARG 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 5.0 0.6 - - - +
11M LEU* 4.0 20.0 - - + -
57M ARG 3.0 17.8 + - - +
58M TYR 3.7 2.5 - - - +
60M GLU* 1.3 70.6 - - - +
62M ILE* 1.3 67.1 + - - +
64M PHE* 3.2 26.6 + - - +
65M LEU* 2.9 43.2 + - + +
113M ASP* 3.1 25.3 + - - -
115M VAL* 3.7 15.4 - - - +
116M SER* 3.0 21.6 + - - +
119M MET* 4.0 25.4 - - + -
128T GLU* 2.8 33.5 + - - +
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Residues in contact with ILE 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ILE* 4.0 11.7 - - + +
11M LEU* 3.7 27.8 - - + +
12M ASN* 3.6 39.0 - - - +
15M LEU* 4.2 10.3 - - + -
58M TYR 2.9 29.9 + - - +
59M ILE 4.0 2.7 - - - +
61M ARG* 1.3 71.3 - - - +
63M LEU* 1.3 61.2 + - - +
65M LEU* 3.3 7.0 + - - +
66M GLU 3.1 4.9 + - - -
67M GLY* 2.9 49.9 + - - -
68M LEU 3.7 6.3 - - - +
69M PRO* 3.7 14.1 - - + -
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Residues in contact with LEU 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ILE* 3.1 41.4 + - + +
60M GLU* 3.7 5.8 - - + +
62M ILE* 1.3 75.4 - - - +
64M PHE* 1.3 62.1 + - - +
66M GLU* 3.0 16.6 + - - +
67M GLY 4.0 9.2 - - - +
68M LEU* 5.8 1.3 - - + -
69M PRO* 3.4 27.6 - - + -
27N LEU* 4.5 0.9 - - + -
30N ARG* 3.9 27.4 - - + +
31N MET* 4.1 20.6 - - + +
34N ASN* 3.9 32.9 + - + +
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Residues in contact with PHE 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 2.9 76.8 + - + +
60M GLU 3.1 14.9 + - - +
61M ARG* 3.2 39.5 + - - +
63M LEU* 1.3 74.0 - - - +
65M LEU* 1.3 60.9 + - + +
66M GLU* 3.0 4.4 + - - +
34N ASN* 4.2 9.7 + - - +
128T GLU* 3.6 22.9 - - + -
131T ILE* 4.5 1.8 - - + -
132T ASP* 3.7 47.8 - - + +
135T GLU* 4.0 5.2 - - - -
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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