Contacts of the helix formed by residues 69 - 92 (chain F) in PDB entry 6JBQ
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 ALA 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASP* 4.7 12.6 - - - +
64F PHE* 3.4 14.2 - - - -
68F SER* 1.3 80.1 - - - +
70F PHE* 1.3 64.6 + - - +
71F TYR* 3.3 10.8 - - + +
72F THR* 3.5 16.2 - - + +
73F TRP 3.9 0.9 + - - -
28H A 3.9 13.4 + - - +
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASP* 4.2 21.2 + - + +
11F VAL* 5.3 7.6 - - + -
22F PHE* 3.6 28.5 - + - -
25F LEU* 3.7 28.5 - - + -
29F TYR* 4.2 20.2 - + + +
57F ALA* 4.9 0.4 - - + -
61F LEU* 3.7 17.9 - - + -
64F PHE* 4.3 9.5 - + + -
69F ALA* 1.3 75.8 - - - +
71F TYR* 1.3 59.2 + - - +
72F THR 3.5 0.2 - - - -
73F TRP* 3.4 38.9 + + - +
74F LEU* 2.9 55.7 + - + +
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Residues in contact with TYR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F TYR* 3.6 35.7 + + - +
32F LYS* 3.8 41.3 + - + +
33F VAL* 6.2 2.7 - - + -
69F ALA* 3.3 7.6 - - + +
70F PHE* 1.3 79.1 - - - +
72F THR* 1.3 58.5 + - - +
74F LEU* 3.5 6.9 + - + +
75F TYR* 2.9 45.9 + + + +
29H A 3.9 50.7 - + + +
30H A 5.2 3.0 + - - -
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F SER* 3.8 11.4 - - - -
69F ALA* 3.5 16.7 - - + +
71F TYR* 1.3 76.1 - - - +
73F TRP* 1.3 62.4 + - - +
75F TYR* 3.5 1.4 - - - +
76F ARG* 2.9 30.0 + - - +
26H C 4.1 17.4 - - - +
27H A 5.5 0.4 - - - -
28H A 3.6 36.8 + - - +
29H A 3.1 40.3 + - - -
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Residues in contact with TRP 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ALA* 3.2 42.4 - - + -
60F ALA 3.3 26.5 - - - -
61F LEU* 3.6 19.3 - - + -
63F SER* 5.8 0.9 - - - -
64F PHE* 3.9 38.9 - + + +
69F ALA 4.1 1.8 - - - +
70F PHE* 3.4 32.9 + + - +
71F TYR 3.3 0.2 - - - -
72F THR* 1.3 83.0 - - - +
74F LEU* 1.3 56.2 + - - +
76F ARG* 3.4 4.4 + - - +
77F ILE* 3.0 45.8 + - + +
25H T 3.6 50.2 + + + +
26H C 4.2 19.7 - + - +
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Residues in contact with LEU 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F PHE* 5.8 1.1 - - + -
29F TYR* 3.9 21.3 - - + -
33F VAL* 3.8 21.1 - - + -
53F ALA* 4.8 2.5 - - + +
54F PHE* 3.7 32.1 - - + -
57F ALA* 4.0 27.1 - - + -
70F PHE* 2.9 41.8 + - + +
71F TYR* 3.9 7.6 - - + +
73F TRP* 1.3 73.3 - - - +
75F TYR* 1.3 59.8 + - - +
77F ILE* 3.8 8.7 - - + +
78F ALA* 2.9 31.4 + - + +
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Residues in contact with TYR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C GLU* 5.5 6.4 + - - +
36F LEU* 3.5 39.6 - - + +
39F ARG* 5.1 3.6 + - - -
40F TYR* 5.6 2.4 + - - -
71F TYR* 2.9 35.2 + + + +
72F THR 3.5 5.8 - - - +
74F LEU* 1.3 76.1 - - - +
76F ARG* 1.3 58.2 + - - +
78F ALA* 3.3 1.6 + - - +
79F VAL* 3.0 51.1 + - + +
29H A 3.4 77.0 + + + +
30H A 5.3 1.6 + - - -
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C LEU* 5.5 8.9 - - - +
72F THR 2.9 17.2 + - - +
73F TRP 3.9 3.1 - - - +
75F TYR* 1.3 77.8 - - - +
77F ILE* 1.3 57.1 + - - +
79F VAL* 3.5 27.1 + - - +
80F ASN* 2.8 60.4 + - - +
83F LYS* 4.9 6.3 - - - +
25G C 5.9 2.6 + - - -
25H T 3.4 31.0 - - + +
26H C 3.7 17.0 + - - +
28H A 5.6 2.0 - - - +
29H A 4.1 25.9 + - - +
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Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ALA* 3.5 33.4 - - + +
56F LYS* 5.1 4.7 - - + -
57F ALA* 3.8 26.7 - - + +
73F TRP* 3.0 51.8 + - + +
74F LEU* 3.8 7.4 - - + +
76F ARG* 1.3 76.8 - - - +
78F ALA* 1.3 56.9 + - - +
80F ASN* 3.8 1.9 - - - +
81F THR* 2.8 35.2 + - + +
25H T 3.6 37.9 - - + +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 3.9 15.9 - - + -
36F LEU* 3.8 14.6 - - + -
37F VAL* 3.7 25.4 - - + +
53F ALA* 4.3 5.4 - - + -
74F LEU* 2.9 19.0 + - + +
75F TYR 3.7 3.8 - - - +
77F ILE* 1.3 78.3 - - - +
79F VAL* 1.3 57.5 + - - +
81F THR* 2.8 19.2 + - - -
82F ALA* 2.9 19.1 + - - +
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 4.1 10.8 - - + -
40F TYR* 3.7 32.8 - - + +
75F TYR* 3.0 40.8 + - + +
76F ARG* 3.8 22.9 - - - +
78F ALA* 1.3 74.7 - - - +
80F ASN* 1.3 58.8 + - - +
82F ALA* 3.3 5.5 + - - +
83F LYS* 2.9 50.5 + - - +
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Residues in contact with ASN 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LYS* 6.1 1.1 - - - +
76F ARG* 2.8 45.4 + - - +
77F ILE* 3.8 3.6 - - - +
79F VAL* 1.3 77.4 - - - +
81F THR* 1.3 58.1 + - + +
83F LYS* 3.4 2.4 + - - +
84F ASN* 2.9 36.1 + - - +
25G C 3.0 41.9 + - - +
24H G 4.1 12.6 - - + +
25H T 2.4 35.5 + - + +
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Residues in contact with THR 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 5.2 0.7 - - - +
49F VAL* 3.4 24.5 - - - +
52F GLU* 4.8 4.7 - - + -
53F ALA* 3.4 27.2 - - + +
56F LYS* 3.7 32.1 - - - +
77F ILE* 2.8 23.3 + - + +
78F ALA* 2.8 18.0 + - - -
80F ASN* 1.3 72.1 - - + +
82F ALA* 1.3 58.5 + - - +
84F ASN* 3.7 7.3 - - + +
85F TYR* 2.9 23.7 + - - +
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Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 3.8 20.2 - - + -
40F TYR* 4.0 24.5 - - + -
41F VAL* 3.9 15.9 - - + +
49F VAL* 4.1 4.2 - - - +
78F ALA 2.9 18.7 + - - +
79F VAL 3.6 4.3 - - - +
80F ASN 3.3 0.2 - - - -
81F THR* 1.3 77.6 + - - +
83F LYS* 1.3 58.1 + - - +
85F TYR* 3.4 2.8 + - - +
86F LEU* 2.9 33.4 + - - +
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Residues in contact with LYS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F TYR* 4.5 18.6 + - + -
76F ARG* 4.9 7.0 - - - +
79F VAL* 2.9 42.4 + - + +
80F ASN* 3.9 1.1 - - - +
82F ALA* 1.3 74.1 - - + +
84F ASN* 1.3 61.1 + - - +
86F LEU* 3.3 15.0 + - + +
87F VAL* 2.9 34.4 + - + +
24G T 4.0 11.2 + - - +
25G C 3.1 75.7 + - + +
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Residues in contact with ASN 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LYS* 4.3 14.1 - - - +
80F ASN* 2.9 25.6 + - - +
81F THR* 3.7 7.8 - - - +
82F ALA 3.3 0.2 - - - -
83F LYS* 1.3 76.6 - - - +
85F TYR* 1.3 57.3 + - - +
87F VAL* 3.3 9.7 + - - +
88F ALA* 2.9 29.3 + - - +
25G C 3.2 23.4 + - - +
26G A 4.0 3.8 + - - -
22H T 4.4 14.3 - - + +
23H T 3.7 16.6 + - - +
24H G 3.6 9.9 + - - -
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Residues in contact with TYR 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ARG* 5.3 4.5 + - - -
41F VAL* 3.6 28.3 - - + -
42F PRO* 4.7 3.1 - - + -
45F ASP* 2.5 45.7 + - + +
48F ASP* 6.4 2.2 - - + -
49F VAL* 4.1 19.7 - - + -
81F THR 2.9 18.0 + - - +
82F ALA 3.7 3.1 - - - +
84F ASN* 1.3 73.2 - - - +
86F LEU* 1.3 60.7 + - - +
88F ALA* 3.4 9.1 + - + -
89F GLN* 2.9 56.4 + - + +
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F TYR* 4.0 31.9 - - + +
41F VAL* 4.8 8.3 - - + -
42F PRO* 5.3 2.0 - - + -
82F ALA 2.9 20.0 + - - +
83F LYS* 3.6 14.4 - - + +
84F ASN 3.3 0.2 - - - -
85F TYR* 1.3 74.4 - - - +
87F VAL* 1.3 60.6 + - + +
89F GLN* 3.4 19.8 + - + +
90F GLY* 2.9 24.6 + - - -
23G T 4.8 9.0 - - - +
24G T 3.6 38.8 - - + +
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LYS* 2.9 21.4 + - + +
84F ASN* 3.7 10.5 - - - +
85F TYR 3.3 0.2 - - - -
86F LEU* 1.3 76.0 - - + +
88F ALA* 1.3 58.3 + - + +
90F GLY* 3.1 3.3 + - - -
91F ARG* 3.0 57.6 + - - +
24G T 3.9 38.6 - - + +
25G C 6.1 3.6 - - + -
21H A 5.6 2.5 - - - +
22H T 6.2 3.6 - - + -
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Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ASN 2.9 17.0 + - - +
85F TYR* 3.9 12.8 - - + +
87F VAL* 1.3 78.2 - - - +
89F GLN* 1.3 57.0 + - - +
91F ARG* 3.4 10.2 + - - +
92F ARG* 3.2 38.3 + - + +
21H A 5.5 5.2 - - - +
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Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ARG* 6.1 3.8 - - - +
42F PRO* 4.2 19.7 - - - +
85F TYR* 2.9 46.0 + - + +
86F LEU* 3.8 21.5 - - + +
88F ALA* 1.3 73.2 - - - +
90F GLY* 1.3 60.8 + - - +
92F ARG* 3.1 32.3 + - + +
93F PRO 5.0 1.5 - - - +
95F SER* 5.5 4.8 + - - -
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Residues in contact with GLY 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 5.5 4.0 - - - -
86F LEU 2.9 15.3 + - - -
87F VAL* 3.1 5.8 + - - -
89F GLN* 1.3 74.9 - - - +
91F ARG* 1.3 63.2 + - - +
92F ARG 3.9 4.2 - - - +
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D TYR* 4.1 21.0 - - - +
87F VAL* 3.0 43.4 + - - +
88F ALA* 3.7 11.5 - - - +
89F GLN 3.2 0.4 - - - -
90F GLY* 1.3 80.2 - - - +
92F ARG* 1.3 68.5 + - - +
93F PRO* 4.0 1.6 - - - +
24G T 6.1 1.4 - - - +
19H T 5.4 1.8 - - - +
20H T 3.5 54.9 + - - +
21H A 3.4 50.8 + - - +
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Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 5.1 8.5 + - - +
42D GLU* 3.4 39.1 + - - +
43D THR 5.4 2.7 - - - +
44D ILE 5.5 3.8 - - - -
46D TYR* 4.6 4.9 - - - -
270D ARG* 4.0 25.3 - - - +
88F ALA* 3.2 28.3 + - + +
89F GLN* 3.1 22.7 + - + +
90F GLY 3.9 4.3 - - - +
91F ARG* 1.3 85.4 - - - +
93F PRO* 1.3 82.4 - - + +
94F PRO* 3.9 2.1 - - - +
21H A 3.6 29.3 + - - -
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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
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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) + - + + + + + -
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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