Contacts of the helix formed by residues 33 - 65 (chain R) in PDB entry 6CMO
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 GLU 33 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ALA* 1.3 75.1 - - - +
34R PRO* 1.3 77.0 - - + +
35R TRP* 3.1 64.3 - - + +
36R GLN* 3.3 26.7 + - + +
37R PHE* 3.3 12.4 - - - -
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Residues in contact with PRO 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R TYR* 4.8 12.3 - - + +
32R ALA 3.8 6.3 - - - +
33R GLU* 1.3 98.8 - - - +
35R TRP* 1.3 65.6 + - + +
37R PHE* 3.2 19.6 - - + -
38R SER* 2.9 30.7 + - - +
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Residues in contact with TRP 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R GLU* 3.1 37.6 - - + +
34R PRO* 1.3 82.1 - - + +
36R GLN* 1.3 79.1 + - + +
38R SER* 3.9 6.1 - - - -
39R MET* 2.9 38.9 + - + +
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Residues in contact with GLN 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R ALA* 3.7 19.7 - - - +
33R GLU* 3.3 31.7 + - + +
35R TRP* 1.3 92.7 - - + +
37R PHE* 1.3 81.5 + - - +
39R MET* 3.8 11.0 - - + +
40R LEU* 2.9 43.9 + - - +
183R LEU* 4.9 8.9 - - - +
289R THR* 5.8 2.9 - - - +
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Residues in contact with PHE 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R TYR* 3.9 34.3 - + - -
32R ALA* 5.4 5.6 - - + -
33R GLU 3.3 12.3 - - - -
34R PRO* 3.2 36.4 + - + -
36R GLN* 1.3 92.2 - - - +
38R SER* 1.3 71.0 + - - +
40R LEU* 3.4 18.6 + - + +
41R ALA* 3.0 27.5 + - + +
98R SER* 5.2 8.3 - - - -
101R GLY* 4.3 20.4 - - - -
183R LEU* 5.1 13.7 - - + -
185R CYS* 6.3 3.6 - - - -
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Residues in contact with SER 38 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R PRO* 2.9 20.7 + - - +
35R TRP* 3.9 6.7 - - - -
37R PHE* 1.3 91.9 - - - +
39R MET* 1.3 56.1 + - - +
41R ALA* 3.2 9.8 + - - +
42R ALA* 3.0 25.1 + - - +
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Residues in contact with MET 39 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R TRP* 2.9 26.4 + - + +
36R GLN* 3.9 11.0 - - + +
38R SER* 1.3 76.7 - - - +
40R LEU* 1.3 58.0 + - - +
42R ALA* 3.1 10.6 + - + +
43R TYR* 2.9 39.7 + - + -
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Residues in contact with LEU 40 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R GLN* 2.9 36.3 + - - +
37R PHE* 3.4 20.2 - - + +
38R SER 3.3 0.2 - - - -
39R MET* 1.3 73.9 - - - +
41R ALA* 1.3 63.4 + - + +
43R TYR* 3.5 37.2 + - + +
44R MET* 2.9 41.0 + - + +
98R SER* 6.2 3.1 - - - -
183R LEU* 5.9 4.5 - - + -
289R THR* 5.4 12.1 - - + -
293R PHE* 5.8 10.1 - - + -
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Residues in contact with ALA 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 3.0 14.4 + - + +
38R SER* 3.2 11.9 + - - +
40R LEU* 1.3 79.4 - - + +
42R ALA* 1.3 62.2 + - - +
44R MET* 3.1 12.3 + - - +
45R PHE* 3.0 19.4 + - - +
95R LEU* 3.9 8.3 - - + +
98R SER* 4.0 31.9 - - - +
99R LEU* 6.0 0.7 - - - -
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Residues in contact with ALA 42 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R SER 3.0 12.9 + - - +
39R MET* 3.1 15.7 + - + +
41R ALA* 1.3 76.4 - - - +
43R TYR* 1.3 58.0 + - - +
45R PHE* 3.2 10.6 + - - +
46R LEU* 3.0 24.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R MET* 2.9 36.1 + - + +
40R LEU* 3.5 31.3 - - + +
42R ALA* 1.3 73.1 - - - +
44R MET* 1.3 86.0 + - + +
45R PHE 3.2 0.2 - - - -
46R LEU* 3.6 16.6 - - + -
47R LEU* 2.8 44.1 + - + +
293R PHE* 3.3 34.8 - + - -
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Residues in contact with MET 44 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R LEU* 2.9 31.9 + - + +
41R ALA* 3.1 12.5 + - - +
43R TYR* 1.3 109.2 - - + +
45R PHE* 1.3 55.7 + - - +
47R LEU* 3.3 12.8 + - + +
48R ILE* 3.0 30.6 + - - +
91R PHE* 6.5 1.3 - - - -
94R THR* 5.1 12.3 - - - +
95R LEU* 4.1 18.3 - - + +
98R SER* 5.6 2.9 - - - +
293R PHE* 4.9 17.7 - - + +
296R LYS* 4.8 18.4 - - + -
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Residues in contact with PHE 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ALA 3.0 11.3 + - - +
42R ALA* 3.2 11.6 + - - +
44R MET* 1.3 76.8 - - - +
46R LEU* 1.3 63.7 + - + +
48R ILE* 3.2 13.3 - - + +
49R VAL* 3.0 51.8 + - + +
95R LEU* 4.2 20.1 - - + +
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Residues in contact with LEU 46 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ALA 3.0 16.1 + - - +
43R TYR* 3.8 13.7 - - + +
45R PHE* 1.3 78.4 - - + +
47R LEU* 1.3 76.7 + - + +
49R VAL* 3.4 12.0 - - + +
50R LEU* 2.9 41.1 + - + +
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Residues in contact with LEU 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R TYR* 2.8 37.0 + - + +
44R MET* 3.7 15.7 - - + +
46R LEU* 1.3 94.9 - - + +
48R ILE* 1.3 60.1 + - - +
50R LEU* 3.4 14.5 + - + +
51R GLY 2.9 21.7 + - - -
297R SER* 5.8 4.0 - - - -
300R ILE* 3.3 51.2 - - + +
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Residues in contact with ILE 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R MET 3.0 18.1 + - - +
45R PHE* 3.2 26.5 - - + +
47R LEU* 1.3 73.8 - - - +
49R VAL* 1.3 65.3 + - + +
51R GLY* 3.8 0.6 - - - -
52R PHE* 3.0 34.5 + - + +
87R VAL* 5.3 16.6 - - + +
88R LEU* 5.7 6.7 - - + -
91R PHE* 5.5 3.8 - - + -
92R THR* 3.8 32.5 - - + +
95R LEU* 5.2 10.8 - - + -
300R ILE* 5.4 0.9 - - - -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R PHE* 3.0 52.3 + - + +
46R LEU* 3.4 14.6 - - + +
48R ILE* 1.3 80.6 - - + +
50R LEU* 1.3 62.3 + - + +
52R PHE* 5.1 2.9 - - - -
53R PRO* 3.3 20.1 - - - +
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Residues in contact with LEU 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R LEU* 2.9 32.0 + - + +
47R LEU* 3.6 20.9 - - + +
48R ILE 3.2 0.2 - - - -
49R VAL* 1.3 78.2 - - - +
51R GLY* 1.3 61.4 + - - +
53R PRO* 3.7 8.7 - - - +
54R ILE* 4.8 5.7 + - - +
300R ILE* 5.7 1.6 - - + -
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Residues in contact with GLY 51 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R LEU 2.9 16.4 + - - -
48R ILE* 3.1 1.8 + - - -
50R LEU* 1.3 77.9 - - - +
52R PHE* 1.3 61.8 + - - +
53R PRO 3.6 0.2 - - - -
54R ILE* 3.3 17.8 - - - +
55R ASN* 3.0 22.1 + - - -
300R ILE* 3.8 20.9 - - - -
----------------------------------------------------------
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Residues in contact with PHE 52 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 3.0 19.5 + - + +
49R VAL* 4.9 2.2 - - - +
51R GLY* 1.3 77.1 - - - +
53R PRO* 1.4 70.3 - - + +
55R ASN* 3.1 10.6 + - - +
56R PHE* 2.9 54.0 + + + -
59R LEU* 5.9 3.4 - - + -
84R LEU* 4.7 20.4 - - + -
88R LEU* 5.1 14.6 - - + -
----------------------------------------------------------
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Residues in contact with PRO 53 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R VAL 3.3 21.3 - - - +
50R LEU 3.7 11.2 - - - +
52R PHE* 1.4 95.9 - - + +
54R ILE* 1.3 55.6 + - - +
56R PHE* 3.6 11.0 - - + +
57R LEU* 2.9 38.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R LEU 4.8 3.8 + - - +
51R GLY* 3.3 21.8 - - - +
53R PRO* 1.3 77.9 - - - +
55R ASN* 1.3 60.0 + - - +
57R LEU* 3.5 10.2 + - + +
58R THR* 2.6 40.9 + - - +
303R PRO* 5.0 11.0 - - + +
304R VAL* 4.2 35.4 - - + +
307R ILE* 5.4 10.5 - - + -
317R MET* 6.3 4.5 - - + -
----------------------------------------------------------
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Residues in contact with ASN 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R GLY* 3.0 23.2 + - - -
52R PHE* 3.1 10.1 + - + +
54R ILE* 1.3 80.2 - - - +
56R PHE* 1.3 59.1 + - - +
58R THR* 3.2 9.6 + - - -
59R LEU* 2.9 33.0 + - - +
80R ALA* 4.7 6.8 - - - +
83R ASP* 5.6 4.0 - - - +
84R LEU* 3.6 43.7 + - + +
87R VAL* 5.0 11.3 - - - +
300R ILE* 6.4 0.4 - - - +
303R PRO* 4.6 20.1 - - - +
----------------------------------------------------------
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Residues in contact with PHE 56 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R PHE* 2.9 39.1 + + + +
53R PRO* 3.3 13.2 + - + +
55R ASN* 1.3 77.1 - - - +
57R LEU* 1.3 69.1 + - + +
59R LEU* 3.1 22.1 + - + +
60R TYR* 2.9 34.7 + + + +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R PRO* 2.9 24.2 + - + +
54R ILE* 3.9 8.3 - - + +
56R PHE* 1.3 84.7 - - + +
58R THR* 1.3 60.1 + - - +
60R TYR* 3.6 9.8 - - + +
61R VAL* 2.9 36.8 + - + +
317R MET* 4.9 26.5 - - + +
320R THR* 4.5 22.4 - - + -
321R ILE* 5.2 22.0 - - + -
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Residues in contact with THR 58 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R ILE* 2.6 27.6 + - - +
55R ASN* 3.3 14.5 + - - -
56R PHE 3.2 0.2 - - - -
57R LEU* 1.3 76.3 - - - +
59R LEU* 1.3 54.3 + - + +
61R VAL* 3.5 5.7 + - - +
62R THR* 2.4 42.8 + - - +
77R LEU* 6.0 1.6 - - - -
80R ALA* 3.9 28.3 - - + -
81R VAL* 6.1 0.7 - - + -
84R LEU* 5.9 0.7 - - + -
307R ILE* 5.0 22.9 - - + +
313R PHE* 6.5 0.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 59 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R PHE* 5.9 3.8 - - + -
55R ASN 2.9 20.3 + - - +
56R PHE* 3.1 24.7 + - + +
58R THR* 1.3 77.6 - - + +
60R TYR* 1.3 58.8 + - - +
62R THR* 3.2 11.5 + - + +
63R VAL* 3.0 35.8 + - + +
81R VAL* 3.8 29.6 - - + -
84R LEU* 4.9 17.7 - - + -
----------------------------------------------------------
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Residues in contact with TYR 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R PHE* 2.9 23.9 + + + +
57R LEU* 3.2 17.0 + - + +
59R LEU* 1.3 75.4 - - - +
61R VAL* 1.3 63.7 + - + +
63R VAL* 5.1 2.9 - - + -
64R GLN* 2.9 73.7 + - + +
65R HIS* 4.8 4.3 - + - -
320R THR* 3.6 37.2 - - + -
----------------------------------------------------------
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Residues in contact with VAL 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R LEU* 2.9 22.8 + - + +
58R THR* 4.0 6.1 - - - +
60R TYR* 1.3 77.3 - - + +
62R THR* 1.3 63.9 + - - +
65R HIS* 3.4 42.2 + - + +
68R LEU* 3.8 29.3 - - + +
313R PHE* 3.8 23.3 - - + +
316R CYS* 4.7 14.8 - - + -
317R MET* 5.0 8.1 - - + +
320R THR* 4.8 9.2 - - + +
----------------------------------------------------------
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Residues in contact with THR 62 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R THR* 2.4 30.9 + - - +
59R LEU* 3.4 15.6 - - + +
61R VAL* 1.3 79.8 - - - +
63R VAL* 1.3 67.6 + - + +
65R HIS 4.4 5.4 - - - +
69R ARG* 5.3 8.1 + - - +
77R LEU* 4.7 29.3 - - + +
81R VAL* 5.7 5.3 - - + +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R LEU* 3.0 20.4 + - + +
60R TYR* 4.5 2.7 - - + +
62R THR* 1.3 83.7 - - + +
64R GLN* 1.3 68.3 + - - +
65R HIS 3.6 1.4 - - - -
66R LYS* 5.1 1.2 + - - +
69R ARG* 5.7 2.8 + - - -
----------------------------------------------------------
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Residues in contact with GLN 64 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R TYR* 2.9 59.8 + - + +
63R VAL* 1.3 81.7 - - + +
65R HIS* 1.3 74.6 + - + +
66R LYS* 3.4 5.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 65 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R TYR* 4.7 4.8 - + - -
61R VAL* 3.4 41.2 + - + +
62R THR 4.4 5.0 - - - +
63R VAL 4.8 1.6 - - - -
64R GLN* 1.3 93.0 - - + +
66R LYS* 1.3 63.2 + - - +
67R LYS* 3.3 12.7 + - + +
68R LEU* 4.0 18.0 + - + +
69R ARG* 4.9 4.2 + - - +
316R CYS* 4.6 21.1 + - + +
319R THR* 6.2 4.0 - - + -
320R THR* 3.9 20.6 + - - -
----------------------------------------------------------
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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