Contacts of the helix formed by residues 38 - 67 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN* 5.0 4.6 - - - +
37G HIS* 3.1 51.3 + - - +
38G ASN* 5.2 4.6 - - - +
36I GLY 2.9 2.0 + - - -
37I HIS* 1.3 82.7 + - - +
39I PHE* 1.3 64.2 + - - +
40I PHE 3.2 3.1 + - - -
41I THR* 3.4 15.5 + - + +
42I LEU* 2.9 42.2 + - + +
95I MET* 3.9 16.2 - - + +
149I PHE* 3.9 13.8 - - + -
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Residues in contact with PHE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TRP* 3.8 31.2 - + - -
145D MET* 3.6 44.2 - - + -
148D ALA* 3.5 19.5 - - + +
149D PHE* 4.2 13.0 - - + +
31I HIS* 4.4 7.9 - + - -
32I TRP 5.6 0.7 - - - -
34I MET* 3.5 40.0 - - + +
36I GLY 2.9 16.8 + - - +
37I HIS 3.4 1.4 - - - -
38I ASN* 1.3 76.9 - - - +
40I PHE* 1.3 72.6 + + + +
43I GLY* 2.9 28.9 + - - -
95I MET* 3.9 9.3 - - - +
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Residues in contact with PHE 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D THR* 3.8 15.3 - - - +
42D LEU* 3.8 29.6 - - + -
45D LYS* 3.8 40.8 - - + -
145D MET* 4.0 36.3 - - + -
146D PHE* 3.6 28.9 - + - -
149D PHE* 3.8 29.4 - + + -
37I HIS 5.0 1.3 + - - +
38I ASN 3.3 0.8 - - - -
39I PHE* 1.3 83.5 - + - +
41I THR* 1.3 63.8 + - + +
43I GLY* 3.9 0.3 - - - -
44I GLU* 3.2 32.7 + - - +
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Residues in contact with THR 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN* 5.5 0.7 - - - +
41D THR* 4.0 20.6 - - + +
37G HIS 5.7 0.4 + - - +
40G PHE* 3.9 17.4 - - - +
41G THR* 3.7 32.5 - - + +
37I HIS 5.0 1.1 - - - +
38I ASN* 4.0 28.3 - - + +
40I PHE* 1.3 79.9 - - + +
42I LEU* 1.3 64.3 + - - +
44I GLU* 3.6 7.9 + - - +
45I LYS* 3.2 22.9 + - - +
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G PHE* 4.6 9.4 - - + -
34I MET* 3.8 18.6 - - + -
38I ASN* 2.9 40.1 + - + +
41I THR* 1.3 81.2 - - - +
43I GLY* 1.3 56.3 + - - +
45I LYS* 3.2 7.7 + - + +
46I MET* 2.8 39.5 + - + +
95I MET* 3.8 16.8 - - - -
99I MET* 3.4 32.1 - - + -
146I PHE* 4.2 14.6 - - + -
149I PHE* 3.6 22.9 - - + -
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Residues in contact with GLY 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I HIS* 2.9 42.4 + - - -
34I MET* 3.6 8.9 - - - -
39I PHE* 2.9 22.3 + - - -
40I PHE* 3.9 0.9 - - - -
42I LEU* 1.3 77.3 - - - +
44I GLU* 1.3 60.4 + - - +
46I MET 3.3 1.0 + - - -
47I ASP* 3.2 11.0 + - - +
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Residues in contact with GLU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 4.2 21.1 - - - +
40I PHE* 3.2 24.0 + - - +
41I THR* 4.0 6.4 - - - +
42I LEU 3.3 0.2 - - - -
43I GLY* 1.3 71.7 - - - +
45I LYS* 1.3 66.1 + - - +
47I ASP* 3.0 25.0 + - - +
48I ASP* 3.1 20.7 + - - +
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Residues in contact with LYS 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G PHE* 3.4 45.7 - - + -
44G GLU* 5.6 7.0 - - - +
41I THR 3.2 12.7 + - - +
42I LEU* 3.2 14.5 + - + +
44I GLU* 1.3 78.5 - - - +
46I MET* 1.3 67.3 + - + +
48I ASP* 3.4 21.5 + - - +
49I LEU* 3.1 27.6 + - + +
142I HIS* 4.7 15.3 + - - -
145I MET* 4.3 16.8 - - - +
146I PHE* 4.0 19.8 - - + -
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Residues in contact with MET 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ILE* 3.3 29.0 - - + +
30I ILE* 3.9 20.0 - - + -
31I HIS* 3.7 21.1 - - + +
34I MET* 3.8 18.2 - - + -
42I LEU* 2.8 25.7 + - + +
44I GLU 3.2 0.4 - - - -
45I LYS* 1.3 73.5 - - + +
47I ASP* 1.3 61.5 + - - +
49I LEU* 4.4 10.1 - - + -
50I TYR* 2.9 30.7 + - - +
99I MET* 3.7 22.2 - - + -
102I LEU* 4.4 9.2 - - + -
146I PHE* 4.0 28.9 - - + -
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Residues in contact with ASP 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I HIS* 5.8 4.2 - - - -
31I HIS* 3.5 23.9 + - - -
43I GLY 3.2 17.0 + - - +
44I GLU* 3.0 18.2 + - - +
46I MET* 1.3 77.4 - - - +
48I ASP* 1.3 66.3 + - - +
50I TYR* 3.4 5.9 + - - +
51I SER* 3.1 26.7 + - - -
58K ASP* 5.8 0.5 - - - +
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Residues in contact with ASP 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLU* 3.1 16.1 + - - +
45I LYS* 3.7 26.1 - - - +
47I ASP* 1.3 79.5 - - - +
49I LEU* 1.3 61.0 + - + +
51I SER* 3.5 6.3 + - - -
52I GLU* 2.9 30.6 + - - +
142I HIS* 6.4 0.4 - - + -
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Residues in contact with LEU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 4.6 3.8 - - + -
27I ILE* 3.9 16.6 - - + +
45I LYS* 3.1 22.9 + - - +
46I MET* 3.9 11.4 - - - +
47I ASP 3.3 0.2 - - - -
48I ASP* 1.3 76.7 - - + +
50I TYR* 1.3 62.4 + - - +
52I GLU* 4.5 2.5 - - - -
53I PHE* 2.8 52.9 + - + +
102I LEU* 3.8 40.4 - - + -
106I LEU* 5.3 2.7 - - + -
142I HIS* 3.1 37.0 - - + +
146I PHE* 4.1 13.7 - - + -
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Residues in contact with TYR 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I THR* 3.3 47.3 + - + +
27I ILE* 3.9 13.1 - - + +
28I HIS* 3.2 51.4 + + + +
46I MET 2.9 19.3 + - - +
47I ASP* 3.4 7.9 - - - +
49I LEU* 1.3 78.1 - - - +
51I SER* 1.3 68.8 + - - +
53I PHE* 4.2 0.2 - - - -
54I GLY* 3.1 21.1 + - - -
21K ASN* 5.5 0.5 + - - -
24K THR* 5.8 3.1 - - - +
50K TYR* 4.8 13.1 + + - -
54K GLY* 6.1 0.5 - - - -
57K MET* 4.7 8.0 - - - +
58K ASP* 5.5 2.5 - - - -
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Residues in contact with SER 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ASP 3.1 12.6 + - - -
48I ASP* 3.9 7.6 - - - -
49I LEU 3.4 0.2 - - - -
50I TYR* 1.3 84.3 - - - +
52I GLU* 1.3 58.9 + - - +
54I GLY* 3.3 2.1 + - - -
55I GLU* 2.9 30.4 + - - +
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ASP 2.9 19.0 + - - +
49I LEU* 4.0 2.8 - - - +
51I SER* 1.3 78.0 - - - +
53I PHE* 1.3 68.9 + - + +
55I GLU* 3.3 19.5 + - - +
56I GLN* 3.2 29.8 + - - +
138I SER* 2.5 32.6 + - - -
142I HIS* 2.9 29.8 + - - -
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Residues in contact with PHE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 4.1 14.5 - - + +
23I PHE* 3.6 37.0 - + + -
24I THR* 4.2 11.7 - - - +
27I ILE* 4.4 2.5 - - + -
49I LEU* 2.8 53.1 + - + +
52I GLU* 1.3 88.9 - - + +
54I GLY* 1.3 61.2 + - - +
56I GLN* 3.5 35.9 + - - +
57I MET* 3.0 27.7 + - - +
106I LEU* 3.9 21.8 - - + -
109I LEU* 4.6 4.7 - - + -
138I SER* 5.1 2.9 - - - -
139I ILE* 4.2 20.4 - - + -
142I HIS* 4.8 4.9 - + - -
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Residues in contact with GLY 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I THR* 4.0 9.5 + - - -
50I TYR* 3.1 17.0 + - - -
51I SER* 3.7 3.6 - - - -
53I PHE* 1.3 77.0 - - - +
55I GLU* 1.3 60.4 + - - +
57I MET* 3.3 14.4 + - - +
58I ASP* 3.1 26.3 + - - +
50K TYR* 5.8 3.8 - - - -
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Residues in contact with GLU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I SER 2.9 18.7 + - - +
52I GLU* 3.3 26.3 - - - +
53I PHE 3.3 0.2 - - - -
54I GLY* 1.3 74.7 - - - +
56I GLN* 1.3 69.9 + - - +
58I ASP* 3.2 9.2 + - - +
59I GLU* 2.3 69.1 + - - +
135I PHE* 4.0 7.7 - - - -
----------------------------------------------------------
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Residues in contact with GLN 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 3.9 4.6 - - + +
52I GLU* 3.2 21.5 + - - +
53I PHE* 3.6 44.6 - - - +
55I GLU* 1.3 87.0 + - - +
57I MET* 1.3 57.2 + - - +
59I GLU* 3.3 1.2 + - - +
60I VAL* 2.9 34.9 + - - +
113I TYR* 2.8 27.2 + - - +
135I PHE* 3.3 62.9 + - + +
138I SER* 5.0 1.6 + - - -
139I ILE* 4.5 0.8 - - - +
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Residues in contact with MET 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 4.3 9.6 - - - +
20I LEU* 3.7 31.6 - - + +
21I ASN* 3.5 38.8 - - - +
24I THR* 5.9 3.4 - - + +
53I PHE 3.0 14.8 + - - +
54I GLY* 3.4 17.3 - - - +
55I GLU 3.2 0.4 - - - -
56I GLN* 1.3 77.9 - - - +
58I ASP* 1.3 58.0 + - - +
60I VAL* 3.2 3.6 + - - +
61I ALA* 2.9 26.0 + - - +
28K HIS* 3.7 29.6 - - + +
32K TRP* 3.7 21.1 - - + -
50K TYR* 4.6 6.5 - - - +
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Residues in contact with ASP 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I GLY 3.1 11.3 + - - +
55I GLU* 3.4 10.7 - - - +
57I MET* 1.3 79.9 - - - +
59I GLU* 1.3 59.4 + - + +
61I ALA* 3.2 5.5 + - - +
62I GLU* 2.9 51.4 + - - +
28K HIS* 3.3 33.4 + - - -
31K HIS* 4.8 5.5 + - - -
32K TRP* 3.5 20.1 + - - -
50K TYR* 5.5 0.9 - - - -
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Residues in contact with GLU 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 4.3 17.9 + - - +
55I GLU* 2.3 50.9 + - - +
56I GLN 3.9 3.4 - - - +
58I ASP* 1.3 74.7 - - - +
60I VAL* 1.3 60.4 + - - +
62I GLU* 4.0 6.1 - - - +
63I ARG* 3.0 30.1 + - - +
131I MET* 3.6 10.2 - - + +
135I PHE* 3.9 20.2 - - + -
----------------------------------------------------------
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Residues in contact with VAL 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I LEU* 3.2 45.0 - - + +
16I GLN* 4.4 6.3 - - + -
17I VAL* 3.7 12.3 - - + +
20I LEU* 4.2 13.7 - - + -
56I GLN 2.9 21.6 + - - +
57I MET* 3.6 5.8 - - - +
59I GLU* 1.3 73.4 - - - +
61I ALA* 1.3 65.1 + - - +
63I ARG* 3.3 2.3 + - - +
64I LEU* 3.0 22.7 + - - +
113I TYR* 5.0 2.0 - - + +
131I MET* 4.2 13.0 - - + -
132I LEU* 5.3 2.9 - - + -
135I PHE* 3.7 22.0 - - + -
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Residues in contact with ALA 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 4.2 12.3 - - + +
57I MET 2.9 13.8 + - - +
58I ASP 3.2 3.6 + - - +
60I VAL* 1.3 76.4 - - - +
62I GLU* 1.3 57.1 + - - +
64I LEU* 3.5 6.2 + - - +
65I LEU* 3.0 33.2 + - - +
71I PRO* 4.3 5.9 - - + +
32K TRP* 3.4 49.4 - - + +
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Residues in contact with GLU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 2.5 48.0 + - - +
144A TRP* 3.9 31.0 - - + -
58I ASP* 2.9 39.6 + - - +
59I GLU* 4.0 3.3 - - - +
61I ALA* 1.3 74.1 - - - +
63I ARG* 1.3 59.4 + - - +
65I LEU* 3.3 10.2 + - + +
66I ALA* 2.8 29.5 + - - +
31K HIS* 4.8 9.4 + - - -
32K TRP* 5.1 5.6 - - + +
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Residues in contact with ARG 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 4.2 5.3 - - - +
137A ALA 4.9 1.8 + - - -
140A ASP* 3.0 42.0 + - - +
141A LYS* 5.4 1.7 - - - +
13I LEU* 4.4 3.1 - - + -
59I GLU 3.0 18.7 + - - +
60I VAL 3.8 3.4 - - - +
62I GLU* 1.3 74.7 - - - +
64I LEU* 1.3 65.5 + - - +
66I ALA* 3.2 14.6 + - - +
67I ILE* 3.1 45.3 + - + +
125I ASP* 3.2 23.0 + - - -
127I VAL* 3.4 31.9 - - - +
128I THR* 3.0 24.4 + - + +
131I MET* 3.8 25.6 - - + -
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Residues in contact with LEU 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LYS* 3.6 41.1 - - + +
13I LEU* 4.1 13.3 - - + +
14I ASN* 3.4 46.4 - - + +
17I VAL* 4.8 3.1 - - + -
60I VAL 3.0 16.8 + - - +
61I ALA 3.6 4.9 - - - +
63I ARG* 1.3 74.6 - - - +
65I LEU* 1.3 61.1 + - - +
67I ILE* 3.3 12.4 + - + +
69I GLY* 2.8 40.3 + - - -
70I SER 4.2 3.1 - - - +
71I PRO* 3.7 20.0 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 4.0 31.6 - - + +
154A PRO* 3.0 25.9 - - + +
61I ALA 3.0 25.5 + - - +
62I GLU* 3.4 9.4 - - - +
63I ARG 3.1 0.2 - - - -
64I LEU* 1.3 77.1 - - - +
66I ALA* 1.3 58.4 + - - +
68I GLY* 3.2 7.6 + - - -
69I GLY 3.6 12.5 + - - +
70I SER* 4.8 0.4 - - - -
71I PRO* 3.5 26.0 - - + -
32K TRP* 3.8 47.3 - - + +
33K TYR* 4.9 7.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 4.0 26.7 - - - +
141A LYS* 4.6 6.1 - - + +
144A TRP* 4.0 16.1 - - + +
154A PRO* 3.8 12.5 - - - +
155A LEU* 4.6 6.9 - - - +
62I GLU 2.8 18.0 + - - +
63I ARG* 3.2 26.7 + - - +
65I LEU* 1.3 75.7 - - - +
67I ILE* 1.3 59.4 + - - +
68I GLY 3.4 0.7 + - - -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 6.0 0.7 - - - -
155A LEU* 3.7 18.5 - - - +
9I THR* 3.9 28.7 - - + -
10I LYS* 3.6 33.7 - - + -
13I LEU* 4.2 13.0 - - + -
63I ARG* 3.1 48.7 + - - +
64I LEU* 3.4 14.6 - - - +
65I LEU 3.2 0.2 - - - -
66I ALA* 1.3 76.2 - - - +
68I GLY* 1.3 57.5 + - - +
125I ASP* 4.2 7.2 - - - +
128I THR* 4.8 0.2 - - - +
----------------------------------------------------------
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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).
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