Contacts of the helix formed by residues 47 - 74 (chain O) in PDB entry 6Y5D
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 GLY 47 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O GLY 3.2 1.0 - - - -
46O ALA* 1.3 77.2 - - - +
48O ALA* 1.3 63.8 + - - +
49O PRO* 3.5 0.4 - - - -
50O VAL* 4.0 6.1 - - - -
51O TYR* 3.1 7.6 + - - +
92P SER* 3.7 8.9 - - - +
119P VAL* 3.1 43.0 - - - +
122P TYR* 4.8 4.7 - - - -
123P THR* 5.7 1.3 - - - -
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Residues in contact with ALA 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O LEU* 3.9 4.3 - - + -
44O VAL* 4.0 6.5 - - + -
45O GLY 3.1 8.6 + - - +
47O GLY* 1.3 76.0 - - - +
49O PRO* 1.3 71.6 - - + +
51O TYR 3.2 1.6 + - - -
52O MET* 3.0 24.6 + - - +
90P ILE* 3.7 26.9 - - + +
91P THR 3.7 14.6 - - - +
92P SER* 4.1 5.8 - - - +
95P ILE* 3.6 17.9 - - + +
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Residues in contact with PRO 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ARG* 4.0 1.6 - - - +
28O VAL* 3.6 19.9 - - + +
31O VAL* 3.6 9.2 - - + +
32O HIS* 3.3 54.5 - - + +
35O LEU* 3.6 13.2 - - + -
45O GLY 3.1 12.8 - - - +
46O ALA 3.4 11.2 - - - +
48O ALA* 1.3 95.9 - - + +
50O VAL* 1.3 55.6 + - - +
53O ALA* 2.8 30.8 + - - +
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Residues in contact with VAL 50 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ARG* 5.2 0.2 - - - -
22O ALA* 4.2 8.7 - - + -
24O LEU* 4.3 0.9 - - - +
28O VAL* 3.7 20.4 - - + -
46O ALA 3.8 11.2 - - - +
47O GLY 3.6 7.0 - - - +
49O PRO* 1.3 75.5 - - + +
51O TYR* 1.3 68.8 + - - +
53O ALA* 3.3 3.6 + - - +
54O ALA 3.2 15.8 + - - -
118P ALA* 3.2 47.1 - - + +
119P VAL* 3.5 3.8 - - + +
122P TYR* 3.5 41.1 - - + -
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Residues in contact with TYR 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O GLY 3.1 14.6 + - - +
48O ALA 3.6 4.3 - - - +
50O VAL* 1.3 80.6 - - - +
52O MET* 1.3 63.9 + - - +
54O ALA* 3.3 4.5 + - - +
55O VAL* 3.3 29.1 + - + +
92P SER* 3.7 21.8 - - - -
95P ILE* 3.3 21.8 - - + -
96P GLN* 3.1 45.9 + - + +
99P VAL* 4.2 4.5 - - + -
111P ALA 4.4 1.6 - - - -
112P VAL* 3.0 29.2 + - - +
115P GLY* 3.3 23.1 - - - -
116P THR* 3.3 22.7 - - - -
119P VAL* 3.6 14.1 - - + +
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Residues in contact with MET 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O VAL* 3.3 15.0 - - + -
35O LEU* 3.9 13.0 - - + -
48O ALA 3.0 13.4 + - - +
49O PRO 3.8 3.1 - - - +
51O TYR* 1.3 78.1 - - - +
53O ALA* 1.3 65.4 + - - +
55O VAL* 3.0 7.1 + - - +
56O LEU* 2.9 34.8 + - + +
71P PHE* 3.3 33.7 - - + +
74P ILE* 3.3 35.7 - - + -
75P ALA* 3.4 26.9 - - + +
95P ILE* 3.8 16.3 - - + +
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Residues in contact with ALA 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 3.6 19.0 - - + +
26O PHE* 4.5 6.2 - - + +
27O PRO 3.8 22.7 - - - +
28O VAL* 3.8 11.0 - - + -
31O VAL* 4.2 8.3 - - + -
49O PRO 2.8 22.4 + - - +
50O VAL 3.3 1.3 + - - +
52O MET* 1.3 73.0 - - - +
54O ALA* 1.3 62.7 + - - +
56O LEU* 3.3 5.4 + - - +
57O GLU* 2.9 25.3 + - - +
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Residues in contact with ALA 54 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 3.4 20.6 - - + +
50O VAL 3.2 4.8 + - - -
51O TYR 3.5 9.6 - - - +
52O MET 3.1 0.6 - - - -
53O ALA* 1.3 77.0 - - - +
55O VAL* 1.3 57.8 + - - +
57O GLU* 3.5 1.6 + - - +
58O TYR* 2.8 29.5 + - - +
114P GLU* 3.6 35.9 - - + +
118P ALA* 3.7 18.4 - - + -
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Residues in contact with VAL 55 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O TYR* 3.4 20.9 - - + +
52O MET* 3.0 9.1 + - - +
54O ALA* 1.3 75.8 - - - +
56O LEU* 1.3 64.9 + - - +
58O TYR* 3.2 5.8 + - - +
59O LEU* 3.0 33.5 + - + +
74P ILE* 3.8 25.8 - - + -
99P VAL* 3.8 24.2 - - + -
103P LEU* 4.7 0.9 - - + -
111P ALA* 3.5 39.9 - - + +
115P GLY* 4.5 0.7 - - - -
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Residues in contact with LEU 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O PHE* 4.9 12.6 - - + -
31O VAL* 4.2 20.0 - - + -
52O MET* 2.9 36.0 + - + +
53O ALA* 3.8 4.5 - - - +
55O VAL* 1.3 75.5 - - - +
57O GLU* 1.3 54.6 + - - +
59O LEU* 3.4 5.0 + - - +
60O THR* 2.7 37.7 + - - -
38P TYR* 4.9 3.8 - - + +
66P PHE* 4.9 1.9 - - + -
67P VAL* 4.2 19.3 - - + +
70P ILE* 3.5 32.1 - - + -
71P PHE* 3.7 31.0 - - + +
74P ILE* 4.4 5.8 - - + -
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Residues in contact with GLU 57 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLY 4.5 2.6 - - - +
24O LEU* 3.3 21.9 - - + +
25O GLN* 2.6 39.9 + - - +
26O PHE* 2.9 21.5 + - + -
53O ALA 2.9 17.0 + - - +
54O ALA 3.8 3.8 - - - +
56O LEU* 1.3 75.3 - - - +
58O TYR* 1.3 60.8 + - - +
60O THR* 3.2 6.3 + - - -
61O ALA* 2.8 29.9 + - + +
45P VAL* 3.8 22.5 - - + +
48P GLN* 5.4 2.3 - - - +
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Residues in contact with TYR 58 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O ALA 2.8 19.1 + - - +
55O VAL* 3.5 5.2 - - - +
57O GLU* 1.3 76.3 - - - +
59O LEU* 1.3 69.9 + - + +
61O ALA* 3.2 8.0 + - + +
62O GLU* 2.9 67.1 + - + +
107P LEU* 3.9 27.3 - - + +
110P HIS* 3.1 45.9 - + + +
111P ALA* 4.1 13.7 - - + -
114P GLU* 4.1 27.4 - - + -
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Residues in contact with LEU 59 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O VAL* 3.0 23.8 + - + +
56O LEU* 4.0 2.9 - - - +
58O TYR* 1.3 87.8 - - + +
60O THR* 1.3 65.7 + - - +
62O GLU* 3.2 4.5 + - - +
63O ILE* 3.1 27.9 + - + +
94O LEU* 4.7 3.7 - - + +
97O LEU* 4.1 22.7 - - + -
66P PHE* 3.9 14.4 - - + -
70P ILE* 3.9 30.7 - - + -
103P LEU* 3.8 40.2 - - + -
107P LEU* 4.3 14.1 - - + -
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Residues in contact with THR 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O PHE* 3.9 25.4 - - + -
56O LEU 2.7 23.6 + - - -
57O GLU* 3.4 7.6 - - - -
59O LEU* 1.3 78.9 - - - +
61O ALA* 1.3 63.0 + - - +
63O ILE* 3.3 2.6 + - - +
64O LEU* 3.0 47.4 + - + +
42P VAL* 4.5 6.3 - - + -
45P VAL* 4.2 3.1 - - + -
63P MET* 3.8 14.3 - - + +
66P PHE* 3.8 11.3 - - - -
67P VAL* 3.8 18.6 - - + +
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Residues in contact with ALA 61 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O GLU* 2.8 19.0 + - + +
58O TYR* 3.2 9.6 + - + +
60O THR* 1.3 76.9 - - - +
62O GLU* 1.3 56.6 + - - +
64O LEU* 3.2 0.8 + - - -
65O GLU* 2.7 40.4 + - - +
45P VAL* 3.5 22.2 - - + -
49P VAL* 4.1 14.8 - - + +
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Residues in contact with GLU 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O TYR* 2.9 60.6 + - + +
59O LEU* 3.2 9.4 + - - +
61O ALA* 1.3 78.0 - - - +
63O ILE* 1.3 63.9 + - - +
65O GLU* 3.8 16.7 - - - +
66O LEU* 3.1 36.0 + - - +
91O ASP* 5.6 1.2 - - - +
94O LEU* 4.4 18.1 - - + +
107P LEU* 4.3 9.4 - - + +
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Residues in contact with ILE 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O LEU 3.1 7.4 + - - +
60O THR 3.8 4.5 - - - +
62O GLU* 1.3 76.9 - - - +
64O LEU* 1.3 59.0 + - - +
66O LEU* 3.4 2.4 + - - +
67O ALA* 2.8 28.0 + - + +
84O LEU* 3.6 25.8 - - + -
87O ALA* 4.0 2.2 - - + +
88O ILE* 4.2 21.3 - - + -
94O LEU* 4.0 25.6 - - + -
98O LEU* 4.0 15.5 - - + -
63P MET* 3.9 11.4 - - + -
66P PHE* 3.4 48.5 - - + -
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Residues in contact with LEU 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O THR* 3.0 36.0 + - + +
61O ALA* 3.8 2.7 - - - +
63O ILE* 1.3 75.8 - - - +
65O GLU* 1.3 57.8 + - - +
67O ALA* 4.2 2.9 - - - -
68O GLY* 2.7 31.4 + - - -
79O ILE* 3.6 15.3 - - + +
84O LEU* 4.7 3.6 - - + -
42P VAL* 3.4 27.1 - - + +
45P VAL* 3.8 5.2 - - + -
46P LEU* 3.5 30.1 - - + +
49P VAL* 4.2 3.4 - - + -
50P HIS* 3.9 0.3 - - - -
55P ILE* 4.0 26.9 - - + -
63P MET* 4.1 21.5 - - + -
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Residues in contact with GLU 65 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ALA* 2.7 21.5 + - - +
62O GLU* 3.8 20.6 - - - +
64O LEU* 1.3 74.2 - - - +
66O LEU* 1.3 62.3 + - + +
69O ASN* 3.0 26.0 + - - +
49P VAL* 3.8 23.5 - - + +
50P HIS* 2.9 38.8 + - + +
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Residues in contact with LEU 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O GLU* 3.1 22.6 + - - +
63O ILE 4.0 0.4 - - - +
65O GLU* 1.3 83.8 - - + +
67O ALA* 1.3 58.4 + - - +
69O ASN* 3.1 19.1 + - + +
70O ALA* 2.8 26.2 + - - +
87O ALA* 3.5 28.6 - - + +
91O ASP* 3.7 20.2 - - + +
94O LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 67 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O ILE 2.8 19.7 + - - +
64O LEU 3.8 3.4 - - - +
66O LEU* 1.3 73.2 - - - +
68O GLY* 1.3 55.4 + - - +
70O ALA* 3.1 3.0 + - - +
71O ALA* 2.7 33.6 + - - +
79O ILE* 3.8 16.8 - - + +
83O HIS* 3.7 18.2 - - - +
84O LEU* 3.7 25.1 - - + -
87O ALA* 3.3 9.1 - - + +
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Residues in contact with GLY 68 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O LEU 2.7 21.9 + - - -
65O GLU 3.2 2.4 + - - -
67O ALA* 1.3 72.7 - - - +
69O ASN* 1.3 62.2 + - - +
71O ALA* 3.2 6.5 + - - +
72O ARG* 3.1 25.5 + - - +
79O ILE* 3.7 12.9 - - - +
50P HIS* 3.7 19.3 - - - -
53P THR* 4.4 6.3 + - - -
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Residues in contact with ASN 69 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65O GLU* 3.0 25.0 + - - +
66O LEU* 3.3 24.3 - - + +
67O ALA 3.1 0.2 - - - -
68O GLY* 1.3 74.7 - - - +
70O ALA* 1.3 60.7 + - - +
72O ARG* 3.0 12.6 + - - +
73O ASP* 2.8 35.5 + - - +
50P HIS* 3.1 23.7 + - - -
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Residues in contact with ALA 70 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O LEU 2.8 14.1 + - - +
67O ALA 3.1 7.6 + - - +
69O ASN* 1.3 75.7 - - - +
71O ALA* 1.3 64.1 + - - +
73O ASP* 3.1 15.0 + - - +
74O ASN* 3.1 26.7 + - - -
83O HIS* 3.7 28.9 - - + +
86O LEU* 4.4 16.6 - - + -
87O ALA* 4.6 3.1 - - - +
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Residues in contact with ALA 71 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O ALA 2.7 16.5 + - - +
68O GLY* 3.4 13.5 - - - +
69O ASN 3.1 0.4 - - - -
70O ALA* 1.3 73.0 - - - +
72O ARG* 1.3 53.4 + - + +
74O ASN* 3.3 5.0 + - - +
75O LYS 3.1 7.6 + - - -
76O LYS* 2.7 33.4 + - - +
78O ARG 3.1 38.6 - - - +
79O ILE* 4.5 0.4 - - + +
83O HIS* 3.5 14.8 + - + +
53P THR* 4.7 3.1 - - + -
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Residues in contact with ARG 72 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O GLY 3.1 11.5 + - - +
69O ASN* 3.0 12.4 + - - +
71O ALA* 1.3 74.4 - - + +
73O ASP* 1.3 59.7 + - - +
74O ASN 3.1 1.6 - - - -
75O LYS* 2.7 29.0 + - - +
76O LYS 4.0 15.3 - - - +
50P HIS* 3.3 38.4 + - - +
51P PRO* 5.2 2.2 - - - +
52P ASP* 2.7 36.9 + - - -
53P THR* 4.0 11.5 + - - +
----------------------------------------------------------
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Residues in contact with ASP 73 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O ASN* 2.8 22.7 + - - +
70O ALA* 3.4 15.9 - - - +
72O ARG* 1.3 76.2 - - - +
74O ASN* 1.3 58.9 + - - +
75O LYS* 2.7 31.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 74 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O ALA 3.1 8.9 + - - +
71O ALA 3.7 7.0 - - - +
72O ARG 3.1 0.4 - - - -
73O ASP* 1.3 81.5 - - - +
75O LYS* 1.3 70.6 + - - +
76O LYS* 2.9 36.1 + - + +
82O ARG* 5.4 2.2 - - - +
83O HIS* 3.5 33.6 + - - +
86O LEU* 4.0 18.5 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il