Contacts of the helix formed by residues 48 - 82 (chain V) in PDB entry 5XTD
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 THR 48 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V PRO* 4.0 7.0 - - - +
47V GLY* 1.3 98.3 + - - +
49V PHE* 1.3 65.8 + - - +
50V LEU* 3.3 6.2 + - - +
51V GLU* 3.4 19.6 + - - +
52V GLY 3.5 6.8 + - - -
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Residues in contact with PHE 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V PRO* 5.6 2.2 - - - -
48V THR* 1.3 72.9 - - - +
50V LEU* 1.3 73.6 + - + +
52V GLY* 3.1 3.8 + - - +
53V VAL* 3.0 47.0 + - + +
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Residues in contact with LEU 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V THR* 3.3 6.1 - - - +
49V PHE* 1.3 88.8 - - + +
51V GLU* 1.3 59.9 + - + +
53V VAL* 3.3 9.5 + - + +
54V ALA* 2.9 25.8 + - - +
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Residues in contact with GLU 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V PRO 2.8 18.9 - - - +
47V GLY* 3.0 18.4 - - - +
48V THR* 3.4 8.2 + - - +
49V PHE 3.3 0.4 - - - -
50V LEU* 1.3 76.4 - - + +
52V GLY* 1.3 66.1 + - - +
54V ALA* 3.0 9.8 + - + +
55V LYS* 2.9 46.5 + - - +
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Residues in contact with GLY 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V VAL* 4.4 8.2 - - - +
46V PRO* 3.4 25.7 - - - +
48V THR 3.5 4.8 + - - -
49V PHE 3.1 8.0 + - - -
51V GLU* 1.3 77.4 - - - +
53V VAL* 1.3 63.0 + - - +
55V LYS* 3.2 5.6 + - - +
56V VAL* 3.0 31.4 + - - +
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Residues in contact with VAL 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49V PHE* 3.0 45.6 + - + +
50V LEU* 3.5 12.6 - - + +
52V GLY* 1.3 78.5 - - - +
54V ALA* 1.3 63.1 + - - +
56V VAL* 4.0 5.4 - - - +
57V GLY* 2.9 21.0 + - - -
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Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50V LEU 2.9 14.6 + - - +
51V GLU* 3.0 14.8 + - + +
53V VAL* 1.3 76.8 - - - +
55V LYS* 1.3 60.1 + - + +
57V GLY* 3.8 1.1 - - - -
58V GLN* 2.9 41.0 + - - +
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Residues in contact with LYS 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40V ARG* 3.1 39.3 - - - +
41V VAL* 5.3 6.7 - - + -
45V PRO 5.8 0.2 - - - -
46V PRO* 3.6 26.6 + - + +
51V GLU* 2.9 46.7 + - - +
52V GLY* 3.7 4.9 - - - +
54V ALA* 1.3 76.6 - - + +
56V VAL* 1.3 65.8 + - + +
57V GLY 3.1 1.3 - - - -
58V GLN* 3.1 13.1 + - - +
59V TYR* 3.0 33.6 + - + -
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Residues in contact with VAL 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V LEU* 4.3 12.6 - - + +
37V ALA* 3.7 26.0 - - + +
38V ALA* 5.9 0.2 - - - -
41V VAL* 3.6 24.7 - - + -
52V GLY 3.0 17.9 + - - +
53V VAL* 4.1 5.2 - - - +
55V LYS* 1.3 75.4 - - - +
57V GLY* 1.3 60.6 + - - +
59V TYR* 3.9 0.5 - - - +
60V THR* 2.9 39.1 + - + +
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Residues in contact with GLY 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V VAL 2.9 17.3 + - - -
54V ALA* 3.8 1.8 - - - -
56V VAL* 1.3 80.5 - - - +
58V GLN* 1.3 56.7 + - - +
60V THR* 3.0 7.1 + - - -
61V PHE* 2.9 30.8 + - - +
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Residues in contact with GLN 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V ALA* 2.9 26.0 + - + +
55V LYS* 3.1 12.3 + - - +
57V GLY* 1.3 77.5 - - - +
59V TYR* 1.3 63.9 + - + +
61V PHE* 3.3 5.0 + - - +
62V THR* 2.9 37.6 + - + +
104V ARG* 4.4 17.5 - - - +
201V CDL 5.8 6.3 - - - +
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Residues in contact with TYR 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V GLY* 3.7 19.5 - - - +
36V ALA* 4.7 4.9 - - + -
37V ALA* 3.9 20.2 - - + +
40V ARG* 2.9 58.7 + - + -
41V VAL* 6.6 0.4 - - + -
55V LYS* 3.0 25.2 + - + +
56V VAL 4.0 2.5 - - - +
58V GLN* 1.3 82.7 - - + +
60V THR* 1.3 63.1 + - - +
62V THR* 2.9 19.8 + - + -
63V ALA* 3.0 12.5 + - - +
201V CDL 3.0 74.0 + - + +
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Residues in contact with THR 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V SER* 4.5 8.4 - - - -
33V GLY* 3.6 8.5 - - - +
34V LEU* 3.4 51.4 - - + +
56V VAL* 2.9 21.4 + - + +
57V GLY* 3.0 10.0 + - - -
59V TYR* 1.3 76.0 - - - +
61V PHE* 1.3 59.7 + - - +
63V ALA* 3.6 1.5 - - - +
64V ALA* 3.0 31.9 + - - +
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Residues in contact with PHE 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V GLY 2.9 20.4 + - - +
58V GLN* 3.6 4.3 - - - +
59V TYR 3.1 0.2 - - - -
60V THR* 1.3 77.3 + - - +
62V THR* 1.3 65.1 + - - +
64V ALA* 3.5 2.7 + - - +
65V ALA* 2.9 34.9 + - + +
104V ARG* 3.1 52.5 - - - +
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Residues in contact with THR 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58V GLN* 2.9 18.1 + - + +
59V TYR* 2.9 12.7 + - + -
61V PHE* 1.3 77.7 - - - +
63V ALA* 1.3 61.1 + - - +
65V ALA* 3.2 5.6 + - - +
66V VAL* 2.9 39.4 + - - +
101V LEU* 5.6 5.8 - - - -
104V ARG* 3.1 33.2 - - + +
201V CDL 3.6 34.5 - - + +
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Residues in contact with ALA 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V ALA* 3.0 39.2 - - + +
30V SER* 4.1 0.2 - - - -
33V GLY* 3.8 13.0 - - - +
59V TYR 3.0 14.9 + - - +
60V THR 3.6 4.3 - - - +
61V PHE 3.1 0.2 - - - -
62V THR* 1.3 85.5 + - - +
64V ALA* 1.3 63.6 + - - +
65V ALA 3.2 0.2 + - - -
66V VAL* 3.2 4.1 + - - +
67V GLY 3.0 18.5 + - - -
201V CDL 4.8 16.3 - - + +
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Residues in contact with ALA 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V THR* 3.5 39.3 - - + +
30V SER* 3.9 10.2 - - - +
60V THR 3.0 16.3 + - - +
61V PHE* 4.2 2.9 - - + +
63V ALA* 1.3 76.9 - - - +
65V ALA* 1.3 62.1 + - - +
67V GLY 3.4 0.2 + - - -
68V ALA* 3.0 18.9 + - - +
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Residues in contact with ALA 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61V PHE* 2.9 33.3 + - + +
62V THR* 3.4 8.5 - - - +
64V ALA* 1.3 78.6 - - - +
66V VAL* 1.3 60.4 + - + +
68V ALA* 3.0 9.8 + - - +
69V VAL* 2.9 32.2 + - + +
100V THR* 5.4 0.9 - - - +
104V ARG* 5.6 3.1 - - - -
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Residues in contact with VAL 66 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V ALA* 5.9 0.4 - - + -
62V THR* 2.9 23.2 + - - +
63V ALA* 3.9 4.0 - - - +
65V ALA* 1.3 73.7 - - + +
67V GLY* 1.3 67.4 + - - +
69V VAL* 3.3 2.2 + - - +
70V PHE* 2.9 25.3 + - + +
97V GLY* 3.8 24.2 - - - +
100V THR* 4.0 18.2 - - - +
101V LEU* 4.1 32.3 - - + -
118V PHE* 5.9 9.4 - - + -
201V CDL 5.6 10.5 - - + -
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Residues in contact with GLY 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V THR* 2.7 51.6 + - - -
29V ALA* 4.1 4.7 - - - +
63V ALA 3.0 13.1 + - - -
64V ALA 3.8 2.5 - - - -
66V VAL* 1.3 76.8 - - - +
68V ALA* 1.3 59.4 + - - +
70V PHE* 3.6 4.8 - - - +
71V GLY 3.0 12.5 + - - -
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Residues in contact with ALA 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V ALA* 4.8 3.1 - - + +
25V THR* 4.4 1.8 - - - -
26V THR* 3.5 18.1 - - + +
64V ALA 3.0 13.8 + - - +
65V ALA* 3.0 11.9 + - - +
67V GLY* 1.3 74.8 - - - +
69V VAL* 1.3 68.0 + - + +
71V GLY* 4.0 0.2 - - - -
72V LEU* 3.0 43.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65V ALA* 2.9 16.5 + - + +
66V VAL 3.3 5.1 + - - +
68V ALA* 1.3 77.3 - - + +
70V PHE* 1.3 55.5 + - - +
72V LEU* 4.0 4.8 - - - +
73V THR* 2.7 45.0 + - + +
96V ALA* 4.0 24.5 - - + +
97V GLY* 4.7 1.3 - - - -
100V THR* 3.6 42.0 - - + +
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Residues in contact with PHE 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V TYR* 4.2 12.3 - + - -
25V THR* 3.9 22.9 - - + -
66V VAL* 2.9 19.3 + - + +
67V GLY* 3.6 4.5 - - - +
69V VAL* 1.3 77.7 - - - +
71V GLY* 1.3 75.5 + - - +
73V THR* 2.7 20.9 + - - -
74V THR* 3.0 28.5 + - + +
90V TYR* 4.3 11.9 - + - -
93V GLY* 3.5 29.4 - - - +
94V GLY* 3.9 3.4 - - - -
97V GLY* 5.0 3.8 - - - -
122V ALA* 3.8 29.6 - - + -
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Residues in contact with GLY 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V TYR* 5.1 1.8 - - - -
18V CYS 5.2 0.2 - - - -
21V LYS 4.2 7.0 - - - -
25V THR* 3.8 20.2 - - - -
67V GLY 3.0 8.7 + - - -
70V PHE* 1.3 89.0 - - - +
72V LEU* 1.3 63.9 + - - +
74V THR* 3.0 20.5 + - - -
75V CYS* 3.0 19.6 + - - -
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Residues in contact with LEU 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V CYS* 3.8 18.8 - - + +
19V HIS* 5.1 1.1 - - - +
22V ALA* 3.6 27.5 - - + +
68V ALA* 3.0 32.4 + - + +
69V VAL* 4.0 4.7 - - - +
71V GLY* 1.3 78.6 - - - +
73V THR* 1.3 59.8 + - + +
75V CYS* 3.9 2.9 - - - +
76V ILE* 2.9 47.7 + - + +
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Residues in contact with THR 73 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69V VAL* 2.7 31.9 + - + +
70V PHE* 2.7 11.6 + - - -
72V LEU* 1.3 76.9 - - + +
74V THR* 1.3 56.1 + - - +
76V ILE* 4.5 6.2 - - + +
77V SER* 2.8 33.3 + - - -
92V LEU* 4.7 3.5 - - - +
93V GLY* 3.3 22.2 + - - -
96V ALA* 4.0 19.0 - - + +
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Residues in contact with THR 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V TYR* 4.4 8.8 + - - -
14V ASP* 4.5 3.7 + - - +
70V PHE* 3.0 25.6 + - + +
71V GLY* 3.0 13.9 + - - -
73V THR* 1.3 75.0 - - - +
75V CYS* 1.3 79.6 + - - +
77V SER* 3.4 4.7 + - - -
78V ALA* 2.9 27.0 + - - +
89V ASN* 4.6 7.6 - - - +
90V TYR* 4.0 34.8 - - + -
93V GLY* 3.6 21.3 - - - +
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Residues in contact with CYS 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V TYR* 5.3 1.3 - - - -
14V ASP* 4.1 16.4 - - - +
15V GLY 3.7 7.1 - - - +
16V THR 4.8 0.2 - - - -
18V CYS* 3.5 30.1 - - + -
21V LYS* 3.3 45.3 - - - -
71V GLY* 3.0 18.6 + - - +
72V LEU 4.0 0.2 - - - +
74V THR* 1.3 86.2 + - - +
76V ILE* 1.3 58.2 + - - +
78V ALA* 3.7 3.6 - - - +
79V HIS* 2.9 27.5 + - - +
----------------------------------------------------------
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Residues in contact with ILE 76 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V CYS* 4.2 15.9 - - + -
72V LEU* 2.9 37.2 + - + +
73V THR* 4.1 4.7 - - + +
75V CYS* 1.3 76.3 - - - +
77V SER* 1.3 63.3 + - - +
78V ALA 3.1 1.6 - - - -
79V HIS* 2.9 8.2 + - + +
80V VAL* 2.9 38.5 + - + +
----------------------------------------------------------
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Residues in contact with SER 77 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73V THR 2.8 23.6 + - - -
74V THR* 3.4 7.1 + - - -
76V ILE* 1.3 80.2 - - - +
78V ALA* 1.3 59.6 + - - +
80V VAL* 3.7 7.1 - - - +
81V ARG* 2.9 33.3 + - - +
89V ASN* 4.1 20.8 + - - +
92V LEU* 4.3 22.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 78 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ASP* 3.1 28.0 - - - +
15V GLY* 4.4 4.7 - - - -
74V THR 2.9 16.8 + - - +
75V CYS 3.7 4.5 - - - +
77V SER* 1.3 77.4 + - - +
79V HIS* 1.3 58.7 + - - +
81V ARG* 4.7 0.7 - - - -
82V GLU* 2.5 37.8 + - - +
84V PRO* 3.9 10.3 - - + +
89V ASN* 3.5 20.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 79 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V GLY* 3.8 22.0 - - - +
16V THR* 5.5 3.4 - - + -
18V CYS* 5.1 6.5 - - - -
75V CYS 2.9 18.2 + - - +
76V ILE* 2.9 9.7 + - + +
78V ALA* 1.3 77.0 - - - +
80V VAL* 1.3 59.4 + - - +
82V GLU* 2.7 35.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76V ILE* 2.9 29.7 + - + +
77V SER* 3.7 7.0 - - - +
79V HIS* 1.3 83.5 - - + +
81V ARG* 1.3 69.8 + - + +
82V GLU* 3.1 8.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77V SER* 2.9 17.3 + - - +
78V ALA* 4.3 2.0 - - - +
80V VAL* 1.3 83.6 - - + +
82V GLU* 1.3 60.0 + - - +
83V LYS* 2.8 54.5 + - + +
86V ASP* 5.1 2.7 - - - +
88V LEU* 3.6 36.8 - - - +
89V ASN* 3.7 20.1 + - - +
92V LEU* 3.9 22.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V GLY* 5.7 1.0 - - - -
78V ALA 2.5 22.1 + - - -
79V HIS* 2.7 50.1 + - - +
80V VAL 3.3 7.9 - - - +
81V ARG* 1.3 72.4 - - - +
83V LYS* 1.3 62.8 + - - +
84V PRO* 3.4 12.3 - - - +
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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
------------------------------------------------------------
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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