Contacts of the helix formed by residues 38 - 67 (chain T) in PDB entry 2BKC
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 ASN 38 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M HIS* 2.9 51.8 + - - +
38M ASN* 5.0 6.3 - - - +
41M THR* 5.4 1.2 - - - +
36T GLY* 3.1 1.8 + - - -
37T HIS* 1.3 83.3 + - - +
39T PHE* 1.3 64.4 + - - +
40T PHE 3.3 2.9 - - - -
41T THR* 3.5 19.5 + - - +
42T LEU* 2.9 40.4 + - + +
95T MET* 3.8 17.5 - - + +
149T PHE* 4.0 11.8 - - + -
38X ASN* 5.5 2.8 - - - +
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Residues in contact with PHE 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T HIS* 4.3 9.4 - + - -
32T TRP 5.6 0.2 - - - -
34T MET* 3.4 40.5 - - + +
36T GLY 3.1 19.1 + - - +
37T HIS 3.3 1.8 - - - -
38T ASN* 1.3 78.0 - - - +
40T PHE* 1.3 77.2 + + - +
43T GLY* 3.0 28.8 + - - -
95T MET* 3.9 9.7 - - - +
144X TRP* 3.7 31.6 - + - -
145X MET* 3.6 42.8 - - + -
148X ALA* 3.7 17.0 - - + -
149X PHE* 4.1 11.2 - - + +
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Residues in contact with PHE 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T HIS 4.7 1.7 + - - +
38T ASN 3.3 0.6 - - - -
39T PHE* 1.3 85.9 - + - +
41T THR* 1.3 62.1 + - - +
43T GLY* 3.9 0.5 - - - -
44T GLU* 3.2 25.3 + - - +
41X THR* 4.6 15.3 - - - +
42X LEU* 3.8 20.0 - - + -
45X LYS* 3.4 43.1 - - + -
145X MET* 4.0 30.7 - - + -
146X PHE* 3.4 40.2 - + - -
149X PHE* 3.8 28.9 - + + -
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Residues in contact with THR 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M HIS 5.5 0.4 - - - +
40M PHE* 3.7 23.3 - - + +
41M THR* 3.8 29.2 + - + +
37T HIS 5.3 1.3 - - - +
38T ASN* 3.8 29.6 - - - +
40T PHE* 1.3 80.0 - - - +
42T LEU* 1.3 63.7 + - + +
44T GLU* 3.5 7.3 + - - +
45T LYS* 3.1 28.4 + - - +
41X THR* 4.5 12.8 - - + +
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Residues in contact with LEU 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M HIS 5.5 0.2 - - - +
40M PHE* 4.0 22.9 - - + -
34T MET* 3.9 15.5 - - + -
38T ASN* 2.9 23.6 + - + +
41T THR* 1.3 83.0 - - + +
43T GLY* 1.3 59.7 + - - +
45T LYS* 3.1 7.7 + - + +
46T MET* 2.8 34.4 + - + +
95T MET* 3.8 24.7 - - + -
99T MET* 3.8 24.2 - - + -
146T PHE* 5.3 0.4 - - + -
149T PHE* 3.6 41.3 - - + -
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Residues in contact with GLY 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T HIS* 3.0 41.4 + - - -
34T MET* 3.4 10.1 - - - -
39T PHE* 3.0 24.3 + - - -
40T PHE 3.9 0.9 - - - -
42T LEU* 1.3 77.2 - - - +
44T GLU* 1.3 58.2 + - - +
46T MET 3.3 1.2 + - - -
47T ASP* 3.2 11.7 + - - -
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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
----------------------------------------------------------
40T PHE 3.2 19.1 + - - +
41T THR* 3.9 5.7 - - - +
42T LEU 3.2 0.2 - - - -
43T GLY* 1.3 73.0 - - - +
45T LYS* 1.3 66.9 + - + +
47T ASP* 3.4 13.7 + - + +
48T ASP* 3.2 33.6 + - - +
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Residues in contact with LYS 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M PHE* 3.8 44.8 - - + -
44M GLU* 4.4 17.5 - - - +
41T THR* 3.1 16.7 + - - +
42T LEU* 3.1 13.6 + - + +
44T GLU* 1.3 77.6 - - + +
46T MET* 1.3 73.8 + - + +
48T ASP* 3.3 21.9 + - - +
49T LEU* 3.0 26.3 + - + +
142T HIS* 5.3 7.1 + - - -
145T MET* 4.4 13.9 - - - +
146T PHE* 4.5 10.9 - - + -
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Residues in contact with MET 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T ILE* 3.4 20.1 - - + +
30T ILE* 4.1 19.5 - - - -
31T HIS* 3.7 26.2 - - + +
34T MET* 3.7 18.4 - - + -
42T LEU* 2.8 24.9 + - + +
43T GLY 3.7 6.7 - - - +
45T LYS* 1.3 80.0 - - + +
47T ASP* 1.3 60.8 + - - +
49T LEU* 3.8 22.0 - - + -
50T TYR* 2.9 31.6 + - - +
99T MET* 4.0 17.9 - - + -
102T LEU* 4.2 12.8 - - + -
146T PHE* 4.2 5.6 - - + -
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Residues in contact with ASP 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T HIS* 5.6 5.5 - - - -
31T HIS* 3.4 24.7 + - - -
43T GLY 3.2 13.2 + - - +
44T GLU* 3.5 15.8 - - + +
45T LYS 3.3 0.4 - - - -
46T MET* 1.3 76.7 - - - +
48T ASP* 1.3 63.9 + - - +
50T TYR* 3.6 6.9 + - - +
51T SER* 3.2 23.7 + - - -
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Residues in contact with ASP 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU* 3.2 24.4 + - - +
45T LYS* 3.6 28.7 + - - +
46T MET 3.3 0.2 - - - -
47T ASP* 1.3 78.7 - - - +
49T LEU* 1.3 66.0 + - + +
51T SER* 3.5 5.7 + - - -
52T GLU* 3.0 26.0 + - - +
142T HIS* 6.5 0.2 - - + -
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Residues in contact with LEU 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T PHE* 5.4 0.4 - - + -
27T ILE* 4.0 14.1 - - + -
45T LYS* 3.0 13.3 + - + +
46T MET* 3.8 24.7 - - + +
48T ASP* 1.3 74.5 - - + +
50T TYR* 1.3 58.2 + - - +
52T GLU* 4.1 2.2 - - - +
53T PHE* 2.7 55.0 + - + +
102T LEU* 4.1 16.8 - - + -
106T LEU* 5.6 1.8 - - + -
142T HIS* 3.3 46.9 - - + +
146T PHE* 3.7 29.6 - - + -
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Residues in contact with TYR 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R ASN* 5.6 0.3 + - - -
24R THR* 5.7 4.2 - - - +
50R TYR* 4.9 11.8 + + - -
54R GLY* 6.0 1.4 - - - -
57R MET* 4.6 7.3 - - - +
58R ASP* 5.7 1.8 - - - -
24T THR* 3.4 49.1 + - + +
25T VAL* 5.3 0.6 - - + +
27T ILE* 3.8 13.6 - - + +
28T HIS* 3.2 50.7 + + + +
46T MET 2.9 18.4 + - - +
47T ASP* 3.7 8.3 - - - +
49T LEU* 1.3 77.5 - - - +
51T SER* 1.3 62.9 + - - +
54T GLY* 3.1 24.4 + - - -
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Residues in contact with SER 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T ASP 3.2 14.8 + - - -
48T ASP* 3.8 5.9 + - - -
49T LEU 3.3 0.2 - - - -
50T TYR* 1.3 83.7 - - - +
52T GLU* 1.3 61.5 + - - +
54T GLY* 4.4 1.1 - - - +
55T GLU* 3.0 34.5 + - - +
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Residues in contact with GLU 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T ASP 3.0 19.0 + - - +
49T LEU* 3.8 6.3 - - - +
51T SER* 1.3 76.9 + - - +
53T PHE* 1.3 67.3 + - + +
55T GLU* 3.3 8.3 + - - +
56T GLN* 3.0 36.8 + - + +
138T SER* 2.4 33.6 + - - -
142T HIS* 2.7 29.8 + - - -
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Residues in contact with PHE 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T LEU* 4.0 16.1 - - + +
23T PHE* 3.8 36.8 - + + -
24T THR* 4.2 9.4 + - - +
27T ILE* 4.4 5.4 - - + -
49T LEU* 2.7 57.9 + - + +
52T GLU* 1.3 80.2 - - + +
54T GLY* 1.3 56.8 + - - +
56T GLN* 3.4 36.5 - - - +
57T MET* 3.1 27.7 + - - +
106T LEU* 3.8 19.5 - - + -
109T LEU* 4.2 5.4 - - + -
139T ILE* 3.8 20.4 - - + -
142T HIS* 4.2 10.5 - + - -
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Residues in contact with GLY 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R TYR* 5.9 3.1 - - - -
24T THR* 3.9 9.0 + - - -
50T TYR* 3.1 19.0 + - - -
51T SER* 3.9 2.0 - - - -
53T PHE* 1.3 70.8 - - - +
55T GLU* 1.3 60.6 + - - +
57T MET* 3.3 14.9 + - - +
58T ASP* 3.0 33.5 + - - +
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Residues in contact with GLU 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51T SER* 3.0 22.9 + - - +
52T GLU* 3.3 6.7 + - - +
54T GLY* 1.3 73.3 - - - +
56T GLN* 1.3 64.6 + - - +
58T ASP* 3.2 21.7 + - - +
59T GLU* 3.0 42.0 + - - +
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Residues in contact with GLN 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T LEU* 4.2 5.7 - - + +
52T GLU* 3.0 36.2 + - + +
53T PHE* 3.4 41.0 - - + +
54T GLY 3.4 0.2 - - - -
55T GLU* 1.3 74.0 - - - +
57T MET* 1.3 57.4 - - - +
59T GLU* 3.3 2.5 + - - +
60T VAL* 2.9 35.0 + - - +
113T TYR* 3.2 26.2 + - - -
135T PHE* 3.6 57.9 + - + +
138T SER* 4.7 1.8 - - - -
139T ILE* 4.3 1.6 - - - +
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Residues in contact with MET 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 3.5 35.4 - - + +
32R TRP* 3.7 18.6 - - + -
50R TYR* 4.5 6.5 - - - +
17T VAL* 4.1 10.2 - - + +
20T LEU* 3.7 30.5 - - + +
21T ASN* 3.4 39.9 - - - +
24T THR* 6.4 1.1 - - + -
53T PHE 3.1 12.3 + - - +
54T GLY* 3.4 16.8 - - - +
56T GLN* 1.3 80.1 - - - +
58T ASP* 1.3 57.3 - - - +
60T VAL* 3.7 2.9 - - - +
61T ALA* 3.0 24.6 + - - +
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Residues in contact with ASP 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 3.7 31.4 + - - -
31R HIS* 5.6 2.4 + - - -
32R TRP* 3.8 11.0 + - - -
47R ASP* 5.7 1.0 - - - +
50R TYR* 5.4 2.6 - - - -
54T GLY 3.0 15.7 + - - +
55T GLU* 3.4 28.7 - - - +
57T MET* 1.3 79.6 - - - +
59T GLU* 1.3 58.7 + - - +
61T ALA* 3.4 4.3 + - - +
62T GLU* 2.9 50.4 + - - +
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Residues in contact with GLU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55T GLU* 3.0 31.0 + - - +
56T GLN* 3.6 4.4 - - - +
58T ASP* 1.3 78.1 - - - +
60T VAL* 1.3 54.5 + - - +
62T GLU* 3.4 14.4 + - - +
63T ARG* 2.8 34.1 + - - +
131T MET* 3.9 11.6 - - + +
135T PHE* 4.0 20.8 - - + -
141V LYS* 5.1 8.3 + - - -
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Residues in contact with VAL 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T LEU* 3.3 39.7 - - + +
16T GLN* 4.3 7.0 - - + -
17T VAL* 3.6 14.8 - - + +
20T LEU* 4.0 15.5 - - + -
56T GLN 2.9 21.2 + - - +
57T MET* 3.7 6.1 - - - +
59T GLU* 1.3 71.4 - - - +
61T ALA* 1.3 67.8 + - - +
63T ARG* 3.0 2.4 + - - +
64T LEU* 2.9 22.9 + - - +
113T TYR* 4.7 3.1 - - + +
131T MET* 4.0 14.3 - - + -
132T LEU* 5.4 4.3 - - + -
135T PHE* 3.8 20.9 - - + -
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Residues in contact with ALA 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R TRP* 3.5 44.0 - - + +
17T VAL* 4.3 14.3 - - + +
57T MET* 3.0 19.6 + - - +
58T ASP 3.6 3.1 - - - +
60T VAL* 1.3 76.5 - - - +
62T GLU* 1.3 58.3 + - - +
64T LEU* 3.5 6.2 - - - +
65T LEU* 3.1 29.5 + - - +
71T PRO* 3.9 7.0 - - + +
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Residues in contact with GLU 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R HIS* 4.4 11.1 + - - -
32R TRP* 4.8 8.1 + - + +
58T ASP* 2.9 38.0 + - - +
59T GLU* 3.8 12.8 - - - +
60T VAL 3.2 0.2 - - - -
61T ALA* 1.3 75.2 - - - +
63T ARG* 1.3 62.2 + - - +
65T LEU* 3.8 11.5 - - + +
66T ALA* 3.2 21.8 + - - +
141V LYS* 3.9 26.9 - - + +
144V TRP* 3.8 34.8 - - + -
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Residues in contact with ARG 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T LEU* 4.0 7.0 - - + -
59T GLU 2.8 17.3 + - - +
60T VAL 3.0 3.8 + - - +
62T GLU* 1.3 73.7 - - - +
64T LEU* 1.3 66.4 + - - +
66T ALA* 3.0 19.9 + - - +
67T ILE* 3.1 37.1 + - + +
125T ASP* 3.0 23.4 + - - -
127T VAL* 3.3 34.7 - - - +
128T THR* 3.0 24.1 + - - +
131T MET* 3.8 27.1 - - + -
136V LYS* 4.1 5.9 - - - +
137V ALA* 5.0 1.4 + - - +
140V ASP* 3.0 41.2 + - - +
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Residues in contact with LEU 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T LYS* 3.4 44.6 - - + +
13T LEU* 4.0 17.2 - - + +
14T ASN* 3.2 39.7 - - + +
17T VAL* 4.7 4.7 - - + -
60T VAL 2.9 11.5 + - - +
61T ALA 3.5 8.5 - - - +
63T ARG* 1.3 78.5 - - - +
65T LEU* 1.3 59.6 + - - +
67T ILE* 3.4 9.4 + - + +
68T GLY 3.4 0.3 + - - -
69T GLY* 2.9 35.2 + - - -
70T SER 4.0 3.4 - - - +
71T PRO* 3.6 22.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R TRP* 3.6 48.0 - - + +
33R TYR* 4.9 5.6 - - + -
61T ALA 3.1 17.3 + - - +
62T GLU* 3.8 9.0 - - - +
63T ARG 3.2 0.2 - - - -
64T LEU* 1.3 80.1 - - - +
66T ALA* 1.3 59.0 + - - +
68T GLY* 3.1 16.8 + - - -
69T GLY 3.5 12.4 + - - +
71T PRO* 3.2 30.3 - - + -
144V TRP* 3.8 34.5 - - + +
154V PRO* 3.3 17.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62T GLU 3.2 15.8 + - - +
63T ARG* 3.0 25.9 + - - +
65T LEU* 1.3 79.6 - - - +
67T ILE* 1.3 59.3 + - - +
68T GLY 3.4 1.3 + - - -
140V ASP* 4.0 29.3 - - - +
141V LYS* 4.5 5.2 - - + +
143V ILE* 6.0 0.3 - - - +
144V TRP* 4.2 15.0 - - + -
154V PRO* 4.1 11.9 - - - +
155V LEU* 4.2 9.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T THR* 3.9 29.4 - - + -
10T LYS* 3.2 36.6 + - + -
13T LEU* 4.1 14.8 - - + -
63T ARG* 3.1 46.8 + - - +
64T LEU* 3.5 13.5 - - - +
65T LEU 3.2 0.2 - - - -
66T ALA* 1.3 77.2 - - - +
68T GLY* 1.3 55.7 + - - +
125T ASP* 4.2 8.5 - - - +
140V ASP* 6.1 0.4 - - - -
155V LEU* 3.7 20.0 - - + +
----------------------------------------------------------
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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).
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