Contacts of the helix formed by residues 38 - 67 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ASN* 5.0 4.0 - - - +
37S HIS* 3.3 54.1 + - - +
38S ASN* 5.0 5.7 - - - +
36U GLY 3.1 1.2 - - - -
37U HIS* 1.3 84.3 + - - +
39U PHE* 1.3 62.8 + - - +
40U PHE 3.2 4.0 - - - -
41U THR* 3.4 15.9 + - + +
42U LEU* 3.1 37.2 + - + +
95U MET* 3.9 20.6 - - + +
149U PHE* 4.0 8.3 - - + -
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Residues in contact with PHE 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P TRP* 4.0 26.7 - + - -
145P MET* 3.8 39.0 - - + -
148P ALA* 3.8 18.2 - - + +
149P PHE* 4.1 10.8 - - + +
31U HIS* 4.4 17.5 - + - -
32U TRP 5.6 0.4 - - - -
34U MET* 3.5 39.7 - - + +
36U GLY 3.2 19.0 + - - +
37U HIS 3.3 1.6 - - - -
38U ASN* 1.3 77.1 - - - +
40U PHE* 1.3 83.8 + + + +
43U GLY* 3.2 19.6 + - - -
95U MET* 3.9 9.5 - - - +
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Residues in contact with PHE 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P THR* 4.1 15.5 - - - +
42P LEU* 3.9 22.4 - - + -
45P LYS* 3.6 42.4 - - + -
145P MET* 3.8 37.2 - - + -
146P PHE* 3.6 28.3 - + - -
149P PHE* 3.7 35.4 - + + -
37U HIS 4.8 1.7 + - - +
38U ASN 3.2 0.4 - - - -
39U PHE* 1.3 88.1 - + - +
41U THR* 1.3 64.1 + - - +
43U GLY* 3.8 0.5 - - - -
44U GLU* 3.2 32.2 + - - +
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Residues in contact with THR 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ASN* 5.7 0.7 - - - +
41P THR* 4.2 29.4 - - + +
37S HIS 5.4 1.9 + - - +
38S ASN* 6.1 0.2 - - - +
40S PHE* 3.9 22.0 - - - +
41S THR* 4.4 15.7 + - + +
37U HIS 5.0 2.2 - - - +
38U ASN* 3.8 30.3 - - + +
40U PHE* 1.3 78.9 - - - +
42U LEU* 1.3 61.9 + - + +
44U GLU* 3.7 10.3 + - - +
45U LYS* 3.2 27.5 + - - +
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Residues in contact with LEU 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S HIS 5.5 0.2 - - - +
40S PHE* 4.0 23.3 - - + -
34U MET* 3.9 15.3 - - + -
38U ASN* 3.1 18.0 + - + +
41U THR* 1.3 83.0 - - + +
43U GLY* 1.3 55.9 + - - +
45U LYS* 3.5 4.9 - - + +
46U MET* 2.7 39.4 + - + +
95U MET* 3.4 26.5 - - + -
99U MET* 4.1 17.0 - - - -
146U PHE* 4.9 5.4 - - + -
149U PHE* 3.4 44.2 - - + -
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Residues in contact with GLY 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31U HIS* 3.4 38.2 - - - -
34U MET* 3.7 5.5 - - - -
39U PHE* 3.2 21.2 + - - -
40U PHE* 3.4 1.3 + - - -
42U LEU* 1.3 76.9 - - - +
44U GLU* 1.3 57.3 + - - +
46U MET* 3.3 2.0 + - - +
47U ASP* 3.0 26.1 + - - -
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Residues in contact with GLU 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LYS* 3.7 25.1 - - - +
40U PHE* 3.2 21.5 + - - +
41U THR* 4.0 7.8 - - - +
43U GLY* 1.3 72.0 - - - +
45U LYS* 1.3 65.9 + - + +
47U ASP* 3.2 12.4 + - - +
48U ASP* 3.1 30.6 + - - +
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Residues in contact with LYS 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S PHE* 3.6 48.3 - - + -
44S GLU* 4.6 13.9 - - - +
41U THR* 3.2 19.7 + - - +
42U LEU* 3.2 10.7 + - + +
44U GLU* 1.3 78.8 - - + +
46U MET* 1.3 63.8 + - + +
48U ASP* 3.5 19.4 + - + +
49U LEU* 3.1 26.5 + - + +
142U HIS* 5.1 10.1 + - - -
145U MET* 4.7 13.1 - - - +
146U PHE* 4.3 17.6 - - + -
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Residues in contact with MET 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U ILE* 3.2 30.9 - - + +
30U ILE* 4.0 21.5 - - + -
31U HIS* 4.1 17.3 - - + +
34U MET* 3.8 20.4 - - + -
42U LEU* 2.7 26.2 + - + +
43U GLY 3.3 5.1 + - - +
45U LYS* 1.3 73.7 - - + +
47U ASP* 1.3 60.9 + - - +
49U LEU* 3.8 17.3 - - + -
50U TYR* 2.9 26.9 + - - +
99U MET* 4.1 7.4 - - + -
102U LEU* 4.0 9.4 - - + -
146U PHE* 3.5 36.6 - - + -
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Residues in contact with ASP 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28U HIS* 5.7 4.0 - - - -
31U HIS* 3.4 28.3 + - - -
43U GLY 3.0 18.2 + - - +
44U GLU* 3.4 16.0 - - - +
46U MET* 1.3 75.9 - - - +
48U ASP* 1.3 61.1 + - - +
50U TYR* 3.6 6.6 - - - +
51U SER* 3.2 28.8 + - - -
58X ASP* 5.7 2.6 - - - +
62X GLU* 5.5 0.3 - - - +
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Residues in contact with ASP 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U GLU* 3.1 16.6 + - - +
45U LYS* 3.6 27.6 + - + +
47U ASP* 1.3 78.1 - - - +
49U LEU* 1.3 61.2 + - + +
51U SER* 3.3 7.3 + - - -
52U GLU* 2.9 29.5 + - - +
142U HIS* 6.5 0.4 - - + -
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Residues in contact with LEU 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U PHE* 4.6 3.6 - - + -
27U ILE* 4.0 15.0 - - + -
45U LYS* 3.1 14.6 + - + +
46U MET* 3.8 24.9 - - + +
48U ASP* 1.3 77.3 - - + +
50U TYR* 1.3 60.9 + - - +
52U GLU* 3.2 3.9 + - - +
53U PHE* 2.9 49.5 + - + +
102U LEU* 3.9 28.5 - - + -
106U LEU* 5.2 2.5 - - + -
142U HIS* 3.2 47.8 - - + +
146U PHE* 4.3 7.9 - - + -
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Residues in contact with TYR 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U THR* 3.3 47.5 + - + +
25U VAL* 6.0 0.2 - - - +
27U ILE* 3.9 15.5 - - + +
28U HIS* 3.1 52.0 + + + +
46U MET 2.9 18.4 + - - +
47U ASP* 3.6 7.9 - - - +
49U LEU* 1.3 77.0 - - - +
51U SER* 1.3 66.5 + - - +
54U GLY* 3.2 21.0 + - - -
21X ASN* 5.1 1.6 + - - -
50X TYR* 5.1 9.5 + + - -
54X GLY* 6.0 1.3 - - - -
57X MET* 4.1 9.5 - - - +
58X ASP* 5.6 2.5 - - - -
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Residues in contact with SER 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47U ASP 3.2 13.3 + - - -
48U ASP* 3.5 10.3 - - - -
49U LEU 3.3 0.2 - - - -
50U TYR* 1.3 85.2 - - - +
52U GLU* 1.3 64.5 + - - +
54U GLY* 3.4 1.4 + - - -
55U GLU* 3.1 23.6 + - - +
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Residues in contact with GLU 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48U ASP 2.9 16.8 + - - +
49U LEU* 3.2 5.5 + - - +
51U SER* 1.3 78.5 - - - +
53U PHE* 1.3 69.7 + - + +
55U GLU* 3.2 8.5 + - - +
56U GLN* 2.9 37.1 + - + +
138U SER* 2.4 32.1 + - - -
142U HIS* 2.9 26.8 + - - -
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Residues in contact with PHE 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U LEU* 4.3 13.2 - - + +
23U PHE* 3.7 31.9 - + + -
24U THR* 4.4 7.8 + - - +
27U ILE* 4.5 5.6 - - + -
49U LEU* 2.9 48.1 + - + +
52U GLU* 1.3 84.5 - - + +
54U GLY* 1.3 59.6 + - - +
56U GLN* 3.4 34.6 - - - +
57U MET* 3.0 27.7 + - - +
106U LEU* 3.6 22.9 - - + -
109U LEU* 4.1 11.4 - - + -
139U ILE* 3.9 20.6 - - + -
142U HIS* 4.2 11.2 - + - -
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Residues in contact with GLY 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U THR* 4.1 9.9 + - - -
50U TYR* 3.2 19.6 + - - -
51U SER* 3.9 1.3 - - - -
53U PHE* 1.3 74.7 - - - +
55U GLU* 1.3 64.3 + - - +
57U MET* 3.5 13.7 + - - +
58U ASP* 3.1 23.2 + - - +
28X HIS* 5.4 1.2 + - - -
50X TYR* 6.0 2.7 - - - -
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Residues in contact with GLU 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U SER 3.1 15.1 + - - +
52U GLU* 3.2 10.1 + - + +
54U GLY* 1.3 74.2 - - - +
56U GLN* 1.3 65.9 + - - +
58U ASP* 3.3 19.8 + - - +
59U GLU* 3.1 51.2 + - - +
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Residues in contact with GLN 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U LEU* 4.3 6.9 - - + +
52U GLU* 2.9 30.2 + - + +
53U PHE* 3.2 42.1 + - + +
55U GLU* 1.3 74.9 - - - +
57U MET* 1.3 62.6 + - - +
59U GLU* 3.2 6.1 + - - +
60U VAL* 2.9 27.0 + - - +
113U TYR* 3.0 30.0 + - - -
135U PHE* 3.6 57.2 + - + +
138U SER* 4.9 1.6 + - - -
139U ILE* 4.3 1.2 - - - +
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Residues in contact with MET 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U VAL* 4.1 10.3 - - - +
20U LEU* 3.6 32.0 - - + +
21U ASN* 3.3 40.8 - - - +
24U THR* 6.0 0.4 - - - +
53U PHE 3.0 12.9 + - - +
54U GLY* 3.5 13.9 - - - +
56U GLN* 1.3 76.4 - - - +
58U ASP* 1.3 65.4 + - - +
60U VAL* 3.1 4.7 + - - +
61U ALA 2.9 19.6 + - - -
28X HIS* 3.4 35.9 - - + +
32X TRP* 3.6 20.4 - - + -
50X TYR* 4.8 4.7 - - - +
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Residues in contact with ASP 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54U GLY 3.1 14.7 + - - +
55U GLU* 3.8 23.2 - - - +
56U GLN 3.3 0.2 - - - -
57U MET* 1.3 85.2 - - - +
59U GLU* 1.3 57.8 + - - +
61U ALA* 3.6 3.5 + - - +
62U GLU* 2.7 57.1 + - - +
28X HIS* 4.2 18.9 - - + +
31X HIS* 4.7 5.0 + - - -
32X TRP* 3.2 24.5 + - - -
47X ASP* 5.5 4.0 - - - +
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Residues in contact with GLU 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M LYS* 4.8 17.3 + - - +
55U GLU* 3.1 41.0 + - - +
56U GLN* 3.7 6.7 + - - +
57U MET 3.2 0.2 - - - -
58U ASP* 1.3 75.6 - - - +
60U VAL* 1.3 61.2 + - - +
62U GLU* 3.7 6.1 - - - +
63U ARG* 2.8 31.5 + - - +
131U MET* 4.0 10.0 - - - +
135U PHE* 3.9 28.5 - - + -
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Residues in contact with VAL 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U LEU* 3.4 42.1 - - + +
16U GLN* 4.6 5.6 - - + -
17U VAL* 3.5 14.8 - - + +
20U LEU* 4.3 12.6 - - + -
56U GLN 2.9 17.9 + - - +
57U MET* 3.5 8.7 - - - +
59U GLU* 1.3 75.6 - - - +
61U ALA* 1.3 57.0 + - - +
63U ARG* 3.2 8.9 + - - +
64U LEU* 2.9 26.9 + - + +
113U TYR* 4.9 2.7 - - + +
131U MET* 4.1 10.8 - - + -
132U LEU* 5.2 2.5 - - + -
135U PHE* 3.6 22.2 - - + -
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Residues in contact with ALA 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U VAL* 4.1 14.1 - - + -
57U MET 2.9 13.4 + - - +
58U ASP 3.8 2.0 - - - +
60U VAL* 1.3 76.7 - - - +
62U GLU* 1.3 59.6 + - - +
64U LEU* 3.5 6.2 + - - +
65U LEU* 3.1 33.7 + - - +
71U PRO* 4.3 7.2 - - + +
32X TRP* 3.5 46.7 - - + -
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Residues in contact with GLU 62 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M LYS* 3.4 38.4 + - - +
144M TRP* 3.5 35.3 - - + -
145M MET* 5.7 0.7 - - - +
58U ASP* 2.7 49.8 + - - +
59U GLU* 3.3 5.4 + - - +
61U ALA* 1.3 74.8 - - - +
63U ARG* 1.3 64.2 + - - +
65U LEU* 3.5 9.2 + - + +
66U ALA* 3.1 23.2 + - - +
31X HIS* 4.5 9.8 + - - -
32X TRP* 4.7 6.5 - - + +
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Residues in contact with ARG 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M LYS* 4.4 3.6 - - - +
137M ALA 5.0 1.4 + - - -
140M ASP* 3.0 40.4 + - - +
141M LYS* 5.5 1.7 - - - +
13U LEU* 4.3 6.7 - - + -
59U GLU 2.8 18.4 + - - +
60U VAL 3.2 5.8 + - - +
62U GLU* 1.3 75.5 - - - +
64U LEU* 1.3 64.5 + - - +
66U ALA* 3.0 21.0 + - - +
67U ILE* 3.2 35.0 + - - +
125U ASP* 2.9 25.7 + - - -
127U VAL* 3.3 35.0 - - - +
128U THR* 2.9 20.7 + - - +
131U MET* 3.7 26.5 - - + -
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Residues in contact with LEU 64 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U LYS* 3.4 38.4 - - + +
13U LEU* 4.2 13.2 - - + +
14U ASN* 3.6 41.3 - - - +
17U VAL* 5.0 3.1 - - + -
60U VAL 2.9 16.3 + - - +
61U ALA 3.7 4.9 - - - +
63U ARG* 1.3 75.6 - - - +
65U LEU* 1.3 60.8 + - - +
66U ALA 3.3 0.3 + - - -
67U ILE* 3.4 10.1 + - + +
68U GLY 3.4 4.5 + - - -
69U GLY* 2.8 43.1 + - - -
70U SER 4.2 0.7 - - - +
71U PRO* 3.7 22.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M TRP* 3.6 42.6 - - + +
154M PRO* 3.2 18.4 - - - +
61U ALA 3.1 22.6 + - - +
62U GLU* 3.5 13.5 - - - +
64U LEU* 1.3 76.4 - - - +
66U ALA* 1.3 57.6 + - - +
68U GLY* 3.1 16.6 + - - -
69U GLY 3.7 11.2 + - - +
71U PRO* 3.5 28.0 - - + -
32X TRP* 3.8 33.9 - - + +
33X TYR* 4.9 6.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ASP* 3.8 33.1 - - + +
141M LYS* 4.5 3.8 - - + +
143M ILE* 6.1 0.5 - - - +
144M TRP* 4.2 14.1 - - + -
154M PRO* 4.0 12.0 - - - +
155M LEU* 4.4 9.9 - - - +
62U GLU 3.1 10.7 + - - +
63U ARG* 3.0 25.0 + - - +
65U LEU* 1.3 80.6 - - - +
67U ILE* 1.3 58.4 + - - +
68U GLY 3.4 1.5 + - - -
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Residues in contact with ILE 67 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ASP* 6.1 0.2 - - - -
155M LEU* 3.5 18.7 - - - +
9U THR* 4.1 26.0 - - + -
10U LYS* 3.6 39.0 + - + +
13U LEU* 4.2 12.3 - - + -
63U ARG* 3.2 45.0 + - - +
64U LEU* 3.4 14.4 - - + +
66U ALA* 1.3 76.4 - - - +
68U GLY* 1.3 57.6 + - - +
125U ASP* 4.1 8.5 - - - +
----------------------------------------------------------
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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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