Contacts of the helix formed by residues 38 - 64 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R ARG* 5.1 9.5 - - - +
157R GLU* 3.0 28.7 + - - +
33T LYS* 5.4 6.7 - - + +
36T GLY* 3.0 18.3 + - - +
37T LEU* 1.3 70.1 - - - +
39T ARG* 1.3 63.8 + - - +
41T ASN* 3.1 9.1 + - - +
42T ASP* 3.0 28.7 + - - +
153T GLN 3.1 5.9 + - - +
154T ILE 3.0 23.0 + - - +
156T GLU* 3.6 32.3 - - - +
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Residues in contact with ARG 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N LYS* 5.0 9.7 - - - +
154N ILE* 5.9 9.0 - - - +
155N ARG* 3.2 25.6 - - - +
38T LYS* 1.3 72.0 - - - +
40T LEU* 1.3 70.4 + - - +
42T ASP* 3.2 5.4 + - - +
43T VAL* 3.1 32.9 + - + +
133T TRP* 3.9 13.9 - - - +
137T GLU* 3.1 39.4 + - - -
152T ALA* 4.0 1.6 - - - -
153T GLN* 2.6 56.1 + - - +
155T ARG 3.7 13.3 + - - +
156T GLU* 4.5 7.6 - - + +
157T GLU* 4.2 24.2 - - + +
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Residues in contact with LEU 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T PHE* 3.7 38.1 - - + -
37T LEU* 3.1 15.7 + - + +
39T ARG* 1.3 85.7 - - - +
41T ASN* 1.3 65.1 + - - +
43T VAL* 4.7 1.6 - - - +
44T GLU* 3.0 30.0 + - - +
83T VAL* 4.2 12.1 - - + -
87T LEU* 5.0 3.1 - - + -
133T TRP* 4.1 20.6 - - + -
149T TYR* 3.6 26.9 - - + +
150T LEU* 5.7 0.2 - - + -
153T GLN* 3.5 38.7 + - + +
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Residues in contact with ASN 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T ALA* 3.1 32.9 - - - +
30T ARG* 2.9 27.7 + - - +
32T PHE* 3.7 1.4 - - - +
33T LYS* 3.4 38.4 - - + +
37T LEU 3.0 9.4 + - - +
38T LYS* 3.4 10.0 - - - +
40T LEU* 1.3 76.1 - - - +
42T ASP* 1.3 76.4 + - - +
45T TYR* 2.9 25.1 + - - +
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Residues in contact with ASP 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T LYS* 3.0 15.4 + - - +
39T ARG* 3.2 5.3 + - - +
41T ASN* 1.3 90.9 + - - +
43T VAL* 1.3 61.2 + - + +
45T TYR* 3.8 3.3 - - - +
46T HIS* 2.7 44.6 + - + +
156T GLU* 3.3 36.2 - - - +
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Residues in contact with VAL 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T ARG* 3.1 27.8 + - + +
40T LEU 4.4 0.9 - - - +
42T ASP* 1.3 74.5 - - + +
44T GLU* 1.3 62.7 + - - +
46T HIS* 3.2 9.2 + - + +
47T GLU* 3.0 29.5 + - + +
133T TRP* 3.5 55.2 - - + +
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Residues in contact with GLU 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T TYR* 3.5 25.4 - - - +
28T HIS* 3.3 19.9 - - - +
29T ALA* 3.9 18.8 - - + +
32T PHE* 3.8 18.3 - - + -
40T LEU 3.0 18.8 + - - +
43T VAL* 1.3 74.5 - - - +
45T TYR* 1.3 64.2 + - - +
47T GLU* 3.1 8.1 + - - +
48T SER* 2.9 21.8 + - - -
87T LEU* 4.6 2.5 - - - -
90T ASP* 2.8 28.5 - - - +
133T TRP* 3.5 27.5 - - + -
134T LEU* 4.1 3.5 - - - +
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Residues in contact with TYR 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T PHE* 3.6 33.0 - + - -
29T ALA* 3.5 11.2 - - + +
30T ARG* 3.7 29.2 - - - +
41T ASN* 2.9 20.8 + - - +
42T ASP* 3.8 3.1 - - - +
44T GLU* 1.3 74.8 - - - +
46T HIS* 1.3 83.3 + + - +
48T SER* 3.1 8.7 - - - -
49T ILE* 3.0 44.2 + - + +
200T HEM 3.6 29.9 + - + +
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Residues in contact with HIS 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T ASP* 2.7 35.2 + - + +
43T VAL* 3.7 8.7 - - + +
45T TYR* 1.3 96.1 - + - +
47T GLU* 1.3 64.7 + - + +
49T ILE* 3.1 11.0 + - + +
50T ASP* 2.9 27.8 + - - +
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Residues in contact with GLU 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T TYR* 3.2 39.0 + - + -
43T VAL* 3.0 21.6 + - + +
44T GLU* 3.1 10.3 + - - +
46T HIS* 1.3 74.4 - - + +
48T SER* 1.3 63.1 + - - +
50T ASP* 3.2 6.6 + - - +
51T GLU* 3.0 28.6 + - - +
130T HIS* 3.5 44.1 - - + +
133T TRP* 3.8 32.5 - - - +
134T LEU* 4.6 1.2 - - - +
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Residues in contact with SER 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T ILE* 3.2 20.9 + - - +
25T TYR* 3.9 9.4 - - - +
26T PHE* 3.4 28.2 - - - -
44T GLU 2.9 11.8 + - - -
45T TYR* 3.1 12.3 - - - -
47T GLU* 1.3 74.6 - - - +
49T ILE* 1.3 62.4 + - - +
51T GLU* 3.1 8.3 + - - +
52T MET* 3.0 41.2 + - - +
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Residues in contact with ILE 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T TYR* 3.0 55.6 + - + +
46T HIS* 3.1 12.3 + - + +
48T SER* 1.3 74.5 - - - +
50T ASP* 1.3 61.6 + - - +
52T MET* 3.2 24.7 - - + +
53T LYS* 2.9 31.4 + - - +
200T HEM 3.8 53.4 - - + +
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Residues in contact with ASP 50 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46T HIS* 2.9 22.3 + - - +
47T GLU* 3.2 9.7 + - - +
49T ILE* 1.3 72.4 - - - +
51T GLU* 1.3 58.5 + - - +
53T LYS* 3.4 16.1 + - - +
54T HIS* 2.9 41.5 + - + +
126T ASP* 5.1 6.9 - - - +
130T HIS* 2.8 33.0 + - + -
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Residues in contact with GLU 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLU* 2.8 12.0 - - - +
21T ALA* 3.9 14.8 - - + +
22T ILE* 3.6 23.2 - - + +
25T TYR* 3.6 10.6 - - + -
47T GLU 3.0 14.5 + - - +
48T SER 3.1 3.1 + - - +
50T ASP* 1.3 71.8 - - - +
52T MET* 1.3 61.3 + - - +
54T HIS* 2.8 15.1 + - - +
55T ALA* 2.8 31.0 + - - +
94T GLU* 3.2 6.9 - - - +
127T GLU* 2.9 2.6 - - - +
130T HIS* 3.4 5.0 + - - -
201T MN 2.0 34.8 + - - -
202T MN 2.0 34.9 + - - -
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Residues in contact with MET 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T ILE* 3.6 22.2 - - + +
26T PHE* 4.1 4.0 - - + -
48T SER* 3.0 33.7 + - - +
49T ILE* 3.2 24.5 - - + +
51T GLU* 1.3 75.2 - - - +
53T LYS* 1.3 57.7 + - - +
55T ALA* 3.2 3.3 + - - +
56T ASP* 2.9 27.0 + - - +
200T HEM 2.2 100.2 - - + +
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Residues in contact with LYS 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ILE* 2.9 27.1 + - - +
50T ASP* 3.6 18.0 + - - +
52T MET* 1.3 73.2 - - - +
54T HIS* 1.3 63.5 + - + +
56T ASP* 3.4 8.8 + - - +
57T ARG* 3.1 25.5 + - - +
200T HEM 3.5 44.4 - - + +
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Residues in contact with HIS 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLU* 3.6 15.5 - - + +
50T ASP* 2.9 27.5 + - + +
51T GLU* 2.8 11.9 + - - +
53T LYS* 1.3 73.5 - - + +
55T ALA* 1.3 65.8 + - - +
57T ARG* 3.0 24.5 + - - +
58T TYR* 3.1 17.5 + - + -
123T ILE* 3.6 29.1 - - + +
126T ASP* 2.8 39.1 + - + -
127T GLU* 3.1 18.4 - - - -
130T HIS* 4.9 0.7 - + - -
202T MN 2.5 23.4 + - - -
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Residues in contact with ALA 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T LEU* 3.8 21.9 - - + +
18T GLU* 4.2 7.7 - - + +
19T LEU* 4.6 3.4 - - + -
22T ILE* 4.0 13.5 - - + -
51T GLU 2.8 16.9 + - - +
52T MET 3.4 9.0 - - - +
54T HIS* 1.3 69.0 - - - +
56T ASP* 1.3 58.6 + - - +
58T TYR* 3.2 8.6 + - - +
59T ILE* 2.9 34.1 + - + +
200T HEM 4.0 14.6 - - + -
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Residues in contact with ASP 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 3.4 25.5 - - + -
30S ARG* 2.9 45.1 + - - +
52T MET 2.9 13.3 + - - +
53T LYS* 3.5 12.6 - - - +
55T ALA* 1.3 75.3 - - - +
57T ARG* 1.3 60.8 + - + +
59T ILE* 3.5 1.9 + - - +
60T GLU* 3.0 34.4 + - - +
200T HEM 4.3 9.8 - - + +
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Residues in contact with ARG 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53T LYS* 3.1 14.7 + - - +
54T HIS* 3.0 16.3 + - - +
56T ASP* 1.3 73.8 - - + +
58T TYR* 1.3 62.6 + - - +
60T GLU* 3.4 4.6 + - - +
61T ARG* 3.0 23.7 + - - +
119T MET* 3.6 39.6 - - + +
122T GLU* 3.0 49.2 + - - +
123T ILE* 4.1 18.9 - - + +
126T ASP* 5.8 1.8 + - - -
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Residues in contact with TYR 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T LEU* 4.2 20.2 - - + +
14T LEU* 3.8 30.0 - - + +
15T LEU* 4.0 26.9 - - + -
18T GLU* 3.7 26.6 + - + -
54T HIS 3.1 20.8 + - - -
55T ALA* 3.7 4.3 - - - +
57T ARG* 1.3 73.1 - - - +
59T ILE* 1.4 58.7 + - - +
61T ARG* 3.1 4.8 + - - -
62T ILE* 2.9 38.9 + - + +
101T LEU* 3.7 22.9 - - - +
119T MET* 3.5 27.6 - - + -
120T MET* 4.4 3.1 - - + +
123T ILE* 3.5 27.4 - - + +
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Residues in contact with ILE 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 3.8 28.7 - - + -
27S LEU* 4.0 9.2 - - + +
30S ARG* 3.9 18.2 - - + -
15T LEU* 4.0 18.8 - - + -
55T ALA 2.9 25.5 + - - +
56T ASP* 3.8 4.9 - - - +
58T TYR* 1.4 71.8 - - - +
60T GLU* 1.3 62.8 + - - +
62T ILE* 3.5 0.8 + - - +
63T LEU* 3.1 41.2 + - + +
69T PRO* 3.8 18.7 - - + +
71T LEU* 3.9 26.2 - - + -
200T HEM 4.4 5.4 - - + -
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Residues in contact with GLU 60 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ARG* 3.2 26.1 + - + +
33S LYS* 3.4 30.4 + - - -
56T ASP* 3.0 42.7 + - - +
57T ARG* 3.9 4.7 - - - +
59T ILE* 1.3 77.2 - - - +
61T ARG* 1.3 60.9 + - - +
63T LEU* 3.5 5.9 + - - +
64T PHE* 3.1 23.2 + - - +
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Residues in contact with ARG 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128K GLU* 3.0 32.5 + - - +
1T MET* 5.0 0.6 - - - +
11T LEU* 3.9 19.7 - - + -
57T ARG 3.0 17.9 + - - +
58T TYR 3.8 2.7 - - - +
60T GLU* 1.3 74.4 - - - +
62T ILE* 1.3 63.8 + - - +
64T PHE* 3.2 26.6 + - - +
65T LEU* 2.9 42.8 + - + +
113T ASP* 3.1 24.9 + - - -
115T VAL* 3.7 15.5 - - - +
116T SER* 3.0 21.4 + - - +
119T MET* 4.0 26.0 - - + -
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Residues in contact with ILE 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8T ILE* 4.0 12.1 - - + +
11T LEU* 3.7 27.6 - - + +
12T ASN* 3.6 38.1 - - - +
15T LEU* 4.2 10.3 - - + -
58T TYR 2.9 28.8 + - - +
59T ILE 4.0 2.9 - - - +
61T ARG* 1.3 70.0 - - - +
63T LEU* 1.3 61.9 + - - +
65T LEU* 3.3 7.2 + - - +
66T GLU 3.2 4.5 + - - -
67T GLY* 2.9 50.6 + - - -
68T LEU 3.7 15.0 - - - +
69T PRO* 3.7 5.6 - - + -
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Residues in contact with LEU 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 4.5 0.9 - - + -
30S ARG* 3.9 31.0 - - + +
31S MET* 4.1 21.3 - - + +
34S ASN* 3.9 29.9 + - + +
59T ILE* 3.1 41.5 + - + +
60T GLU* 3.7 5.4 - - - +
62T ILE* 1.3 74.8 - - - +
64T PHE* 1.3 62.0 + - - +
66T GLU* 3.0 16.6 + - - +
67T GLY 4.0 9.1 - - - +
68T LEU* 5.8 1.8 - - + -
69T PRO* 3.4 27.1 - - + -
----------------------------------------------------------
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Residues in contact with PHE 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128K GLU* 3.8 23.3 - - + -
131K ILE* 4.7 1.8 - - + -
132K ASP* 3.7 46.0 - - + +
135K GLU* 4.0 12.1 - - - -
34S ASN* 4.2 9.7 + - - +
1T MET* 2.9 71.6 + - + +
60T GLU 3.1 13.9 + - - +
61T ARG* 3.2 38.6 - - - +
63T LEU* 1.3 74.6 - - - +
65T LEU* 1.3 62.1 + - + +
66T GLU* 3.0 4.6 + - - +
----------------------------------------------------------
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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