Contacts of the helix formed by residues 38 - 67 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS* 2.8 51.8 + - - +
38N ASN* 4.8 5.7 - - - +
36R GLY 3.1 1.0 - - - -
37R HIS* 1.3 89.6 + - - +
39R PHE* 1.3 56.0 + - - +
40R PHE 3.2 3.5 + - - -
41R THR* 3.4 12.6 + - + +
42R LEU* 2.9 46.0 + - + +
95R MET* 3.3 20.3 - - + +
149R PHE* 3.9 12.4 - - + -
38V ASN* 4.5 7.7 - - - +
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Residues in contact with PHE 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R HIS* 4.3 7.0 - + - -
32R TRP 5.6 0.2 - - - -
34R MET* 3.4 41.7 - - + +
36R GLY 2.9 20.3 + - - +
37R HIS 3.4 1.8 - - - -
38R ASN* 1.3 77.2 - - - +
40R PHE* 1.3 76.3 + + + +
43R GLY* 3.0 27.8 + - - -
95R MET* 3.5 9.6 - - + +
144V TRP* 3.8 31.6 - + - -
145V MET* 3.5 49.6 - - + -
148V ALA* 3.8 11.7 - - + -
149V PHE* 4.2 11.0 - - + +
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Residues in contact with PHE 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R HIS 4.9 1.9 + - - +
38R ASN* 3.2 0.8 - - - +
39R PHE* 1.3 95.8 - + - +
41R THR* 1.3 62.5 + - + +
43R GLY* 3.8 0.3 - - - -
44R GLU* 3.2 27.2 + - - +
41V THR* 3.9 16.2 - - - +
42V LEU* 4.3 14.6 - - + -
45V LYS* 3.6 39.3 - - + -
145V MET* 3.9 26.5 - - + -
146V PHE* 3.7 37.7 - + - -
149V PHE* 3.9 33.9 - + + -
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Residues in contact with THR 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS 5.7 2.9 + - - +
38N ASN* 6.2 0.9 - - - +
40N PHE* 4.0 22.6 - - - +
41N THR* 4.7 12.8 + - + -
37R HIS 5.4 1.8 - - - +
38R ASN* 3.4 19.0 + - + +
40R PHE* 1.3 72.5 - - + +
42R LEU* 1.3 71.7 + - - +
44R GLU* 3.6 19.2 + - - +
45R LYS* 3.1 24.6 + - - +
149R PHE* 6.0 0.3 - - - -
38V ASN* 5.7 1.6 - - - +
41V THR* 3.7 33.7 - - + +
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Residues in contact with LEU 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N PHE* 4.3 20.0 - - + -
34R MET* 3.6 15.5 - - + -
38R ASN* 2.9 17.5 + - + +
41R THR* 1.3 78.6 - - - +
43R GLY* 1.3 59.5 + - - +
45R LYS* 3.2 4.7 + - + +
46R MET* 2.9 37.5 + - + +
95R MET* 3.3 38.4 - - + -
99R MET* 3.8 27.8 - - + -
146R PHE* 4.9 2.5 - - + -
149R PHE* 3.8 35.0 - - + -
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Residues in contact with GLY 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R HIS* 3.2 34.8 + - - -
34R MET* 3.6 11.8 - - - -
39R PHE* 3.0 24.1 + - - -
40R PHE 3.4 1.1 + - - -
41R THR 3.3 0.2 - - - -
42R LEU* 1.3 76.2 - - - +
44R GLU* 1.3 63.0 + - - +
46R MET* 3.3 2.4 + - - -
47R ASP* 3.2 10.6 + - - -
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Residues in contact with GLU 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N PHE* 5.9 1.0 - - - +
44N GLU* 4.7 12.4 - - - +
40R PHE 3.2 14.3 + - - +
41R THR* 3.7 26.6 + - - +
43R GLY* 1.3 78.3 - - - +
45R LYS* 1.3 74.1 + - + +
47R ASP* 3.2 21.7 + - - +
48R ASP* 3.2 20.1 + - - +
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Residues in contact with LYS 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N PHE* 3.5 51.9 - - + -
44N GLU* 4.6 11.9 - - - +
41R THR 3.1 20.8 + - - +
42R LEU* 3.2 7.1 + - - +
44R GLU* 1.3 88.5 - - + +
46R MET* 1.3 67.6 + - + +
48R ASP* 3.3 21.1 + - - +
49R LEU* 3.0 33.1 + - - +
142R HIS* 4.9 11.3 + - - -
145R MET* 4.8 11.1 - - - +
146R PHE* 4.5 10.5 - - + -
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Residues in contact with MET 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ILE* 3.2 23.4 - - + +
30R ILE* 3.8 35.2 - - + -
31R HIS* 3.9 19.1 - - + +
34R MET* 4.2 6.3 - - + -
42R LEU* 2.9 24.7 + - + +
43R GLY 3.7 5.4 - - - +
44R GLU 3.2 0.4 - - - -
45R LYS* 1.3 77.0 - - + +
47R ASP* 1.3 60.4 + - - +
49R LEU* 4.3 7.9 - - + -
50R TYR* 2.8 25.5 + - - +
99R MET* 4.3 6.7 - - + -
102R LEU* 3.8 20.4 - - + -
146R PHE* 3.7 33.2 - - + -
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Residues in contact with ASP 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 5.4 7.3 - - - -
31R HIS* 3.1 32.5 + - - -
43R GLY 3.2 7.5 + - - +
44R GLU* 3.2 15.1 + - - +
46R MET* 1.3 76.6 - - - +
48R ASP* 1.3 64.1 + - - +
50R TYR* 3.4 7.2 + - - +
51R SER* 3.1 26.0 + - - -
58T ASP* 5.7 1.0 - - - +
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Residues in contact with ASP 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLU* 3.2 18.9 + - - +
45R LYS* 3.7 27.1 - - + +
46R MET 3.3 0.2 - - - -
47R ASP* 1.3 76.1 - - - +
49R LEU* 1.3 70.4 + - + +
50R TYR 3.3 0.2 + - - -
51R SER* 3.3 7.2 + - - -
52R GLU* 2.9 25.6 + - - +
142R HIS* 6.3 0.9 - - + -
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Residues in contact with LEU 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 4.8 0.7 - - + -
27R ILE* 3.9 16.8 - - + -
45R LYS* 3.0 23.9 + - - +
46R MET* 3.8 12.8 - - + +
48R ASP* 1.3 78.0 - - + +
50R TYR* 1.3 62.9 + - - +
52R GLU* 4.4 3.1 - - - +
53R PHE* 3.0 49.2 + - + +
102R LEU* 3.8 40.4 - - + -
106R LEU* 5.2 2.5 - - + -
142R HIS* 3.3 36.1 - - + +
146R PHE* 3.9 15.3 - - + -
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Residues in contact with TYR 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R THR* 3.4 52.9 + - + +
27R ILE* 3.8 12.0 - - + +
28R HIS* 3.2 48.2 + + + -
46R MET 2.8 19.3 + - - +
47R ASP* 3.5 9.0 - - - +
48R ASP 3.2 0.2 - - - -
49R LEU* 1.3 75.9 - - - +
51R SER* 1.3 68.7 + - - +
54R GLY* 3.0 22.2 + - - -
21T ASN* 5.5 1.0 + - - -
24T THR* 6.0 2.3 - - - +
50T TYR* 4.9 11.4 + + - -
54T GLY* 5.9 2.6 - - - -
57T MET* 4.5 6.4 - - - +
58T ASP* 5.4 2.0 - - - -
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Residues in contact with SER 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R ASP 3.1 11.3 + - - -
48R ASP* 3.6 9.4 - - - -
50R TYR* 1.3 83.8 - - - +
52R GLU* 1.3 64.1 + - - +
54R GLY* 3.7 1.1 - - - -
55R GLU* 2.9 25.2 + - - +
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Residues in contact with GLU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ASP 2.9 20.4 + - - +
49R LEU* 3.9 4.2 - - - +
51R SER* 1.3 73.2 - - - +
53R PHE* 1.3 68.5 + - + +
55R GLU* 3.0 11.1 + - + +
56R GLN* 2.9 36.0 + - + +
138R SER* 2.5 29.8 + - - -
142R HIS* 2.8 29.7 + - - -
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Residues in contact with PHE 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R LEU* 4.1 13.4 - - + +
23R PHE* 3.6 35.9 - + + -
24R THR* 4.2 11.2 - - - +
27R ILE* 4.5 3.1 - - + -
49R LEU* 3.0 40.6 + - + +
52R GLU* 1.3 89.3 - - + +
54R GLY* 1.3 61.1 + - - +
56R GLN* 3.5 36.2 - - - +
57R MET* 2.8 29.1 + - - +
106R LEU* 3.7 23.3 - - + -
109R LEU* 4.4 4.7 - - + -
139R ILE* 3.9 20.9 - - + -
142R HIS* 4.4 8.3 - + - -
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Residues in contact with GLY 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R THR* 3.9 10.1 + - - -
50R TYR* 3.0 18.7 + - - -
51R SER* 3.7 1.8 - - - -
53R PHE* 1.3 72.9 - - - +
55R GLU* 1.3 63.2 + - - +
57R MET* 3.3 12.7 + - - +
58R ASP* 3.1 28.7 + - - -
50T TYR* 6.0 1.3 - - - -
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Residues in contact with GLU 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R SER 2.9 14.8 + - - +
52R GLU* 3.0 13.2 + - + +
54R GLY* 1.3 72.2 - - - +
56R GLN* 1.3 64.7 + - - +
58R ASP* 3.3 18.8 + - - +
59R GLU* 2.8 55.5 + - - +
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Residues in contact with GLN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R LEU* 4.1 5.8 - - + +
52R GLU* 2.9 27.6 + - + +
53R PHE* 3.5 43.3 - - - +
54R GLY 3.3 0.2 - - - -
55R GLU* 1.3 74.1 - - - +
57R MET* 1.3 65.6 + - - +
59R GLU* 3.0 4.1 + - - +
60R VAL* 2.9 28.3 + - - +
113R TYR* 2.9 27.2 + - - -
135R PHE* 3.6 61.2 + - + +
138R SER* 5.0 0.8 + - - -
139R ILE* 4.2 1.2 - - - +
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Residues in contact with MET 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R VAL* 4.1 8.5 - - - +
20R LEU* 3.5 32.1 - - + +
21R ASN* 3.2 43.5 - - - +
24R THR* 5.9 4.9 - - + +
53R PHE 2.8 17.7 + - - +
54R GLY* 3.5 11.0 - - - +
55R GLU 3.2 0.2 - - - -
56R GLN* 1.3 78.1 - - - +
58R ASP* 1.3 63.2 + - - +
60R VAL* 3.3 3.1 + - - +
61R ALA* 3.2 19.2 + - - +
28T HIS* 3.7 28.9 - - + +
32T TRP* 3.9 21.1 - - + -
50T TYR* 4.6 6.3 - - - +
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Residues in contact with ASP 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R GLY 3.1 18.0 + - - +
55R GLU* 3.6 21.9 - - - +
57R MET* 1.3 78.4 - - - +
59R GLU* 1.3 59.0 + - + +
61R ALA* 3.6 5.1 + - - +
62R GLU* 3.0 45.6 + - - +
28T HIS* 3.0 40.3 + - - -
32T TRP* 4.4 7.2 + - - +
50T TYR* 5.7 1.6 - - - -
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Residues in contact with GLU 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R GLU* 2.8 45.1 + - - +
56R GLN 3.6 6.7 - - - +
58R ASP* 1.3 77.1 - - + +
60R VAL* 1.3 58.6 + - - +
62R GLU* 3.9 8.7 - - - +
63R ARG* 3.0 30.3 + - - +
131R MET* 3.8 11.7 - - - +
135R PHE* 3.5 29.7 - - + -
141X LYS* 6.1 1.8 - - - +
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Residues in contact with VAL 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LEU* 3.3 43.7 - - + +
16R GLN* 4.4 5.8 - - + -
17R VAL* 3.7 12.6 - - + +
20R LEU* 4.0 15.9 - - + -
56R GLN 2.9 16.8 + - - +
57R MET 3.6 7.9 - - - +
58R ASP 3.3 0.2 - - - -
59R GLU* 1.3 76.9 - - - +
61R ALA* 1.3 57.7 + - - +
63R ARG* 3.2 4.0 + - - +
64R LEU* 2.9 26.9 + - - +
113R TYR* 4.8 2.7 - - + +
131R MET* 4.1 11.7 - - + -
132R LEU* 5.3 2.9 - - + -
135R PHE* 3.8 21.5 - - + -
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Residues in contact with ALA 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R VAL* 3.9 15.0 - - + +
57R MET 3.2 10.6 + - - +
58R ASP 3.9 2.7 - - - +
60R VAL* 1.3 79.4 - - - +
62R GLU* 1.3 57.7 + - - +
64R LEU* 3.3 5.7 + - - +
65R LEU* 3.0 35.3 + - - +
71R PRO* 4.3 7.6 - - + +
32T TRP* 3.6 45.5 - - + +
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Residues in contact with GLU 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R ASP* 3.0 33.3 + - - +
59R GLU* 4.0 7.9 - - - +
61R ALA* 1.3 76.1 - - - +
63R ARG* 1.3 62.0 + - - +
65R LEU* 3.5 10.3 + - + +
66R ALA* 3.1 21.8 + - - +
31T HIS* 4.4 16.3 + - - -
32T TRP* 5.0 8.4 + - + +
141X LYS* 2.8 39.2 + - + +
144X TRP* 3.7 34.4 - - + -
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Residues in contact with ARG 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LEU* 4.2 8.1 - - + -
59R GLU 3.0 17.9 + - - +
60R VAL 3.6 3.8 - - - +
62R GLU* 1.3 78.4 - - - +
64R LEU* 1.3 61.3 + - - +
66R ALA* 3.1 12.3 + - - +
67R ILE* 3.1 45.3 + - + +
125R ASP* 2.9 25.9 + - - -
127R VAL* 3.2 32.9 - - - +
128R THR* 3.3 21.0 + - - +
131R MET* 4.0 21.5 - - + -
136X LYS* 4.9 3.0 - - - +
137X ALA 5.1 1.0 + - - -
140X ASP* 2.8 40.8 + - - +
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Residues in contact with LEU 64 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R LYS* 3.4 43.1 - - + +
13R LEU* 4.0 14.5 - - + +
14R ASN* 3.5 40.2 - - + +
17R VAL* 4.8 2.9 - - + -
60R VAL 2.9 13.1 + - - +
61R ALA* 3.3 8.0 + - - +
63R ARG* 1.3 76.3 - - - +
65R LEU* 1.3 61.8 + - - +
67R ILE* 3.2 15.3 + - + +
68R GLY 3.3 0.3 + - - -
69R GLY* 2.9 36.1 + - - -
70R SER 4.1 3.6 - - - +
71R PRO* 3.6 24.0 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R ALA 3.0 27.4 + - - +
62R GLU* 3.6 7.0 - - - +
64R LEU* 1.3 76.5 - - - +
66R ALA* 1.3 59.6 + - - +
68R GLY* 3.3 7.3 + - - -
69R GLY 3.8 10.9 - - - +
70R SER* 4.8 0.2 - - - -
71R PRO* 3.2 30.3 - - + -
32T TRP* 3.8 49.6 - - + +
33T TYR* 4.9 5.8 - - + -
144X TRP* 4.1 30.3 - - + +
154X PRO* 3.0 26.8 - - - +
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Residues in contact with ALA 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU 3.1 13.5 + - - +
63R ARG* 3.1 30.3 + - - +
65R LEU* 1.3 78.4 - - - +
67R ILE* 1.3 58.8 + - - +
68R GLY 3.3 1.3 + - - -
140X ASP* 4.2 24.5 - - + +
141X LYS* 4.6 4.7 - - + +
143X ILE* 5.9 0.9 - - - +
144X TRP* 4.1 15.0 - - + +
154X PRO* 4.0 5.1 - - - +
155X LEU* 3.8 19.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 3.8 29.8 - - + -
10R LYS* 4.2 32.0 + - + -
13R LEU* 3.9 17.9 - - + -
63R ARG* 3.1 43.0 + - - +
64R LEU* 3.3 13.9 - - - +
66R ALA* 1.3 77.0 - - - +
68R GLY* 1.3 56.3 + - - +
69R GLY 3.8 0.3 + - - -
123R GLU* 6.0 0.4 - - - +
125R ASP* 4.1 7.4 - - - +
128R THR* 4.6 0.2 - - - +
155X LEU* 3.7 18.0 - - + +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il