Contacts of the helix formed by residues 45 - 70 (chain I) in PDB entry 1DZG
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 45 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ILE* 5.7 0.2 - - - -
43I ALA 4.0 2.4 + - - -
44I THR* 1.3 72.9 - - - +
46I ARG* 1.3 61.2 + - - +
47I ARG* 3.0 22.1 + - - +
48I VAL* 3.0 38.3 + - + +
49I TRP* 2.8 32.1 + - - +
125I LYS* 3.2 46.1 + - - +
129I ARG* 3.6 18.2 - - - +
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Residues in contact with ARG 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ILE* 4.8 11.4 - - + -
44I THR 3.3 6.2 + - - +
45I ASN* 1.3 72.6 + - - +
47I ARG* 1.3 63.5 + - - +
49I TRP* 3.7 5.5 - - - +
50I GLU* 3.0 40.2 + - + +
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Residues in contact with ARG 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ASN* 3.0 18.8 + - - +
46I ARG* 1.3 79.2 - - - +
48I VAL* 1.3 61.5 + - - +
50I GLU* 4.1 6.5 - - - +
51I LEU* 3.3 21.7 + - - +
121I PHE* 5.1 2.9 - - + -
122I PHE* 4.0 38.1 - - + -
125I LYS* 4.3 15.5 - - + +
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Residues in contact with VAL 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I THR* 6.4 0.9 - - + -
45I ASN* 3.0 37.1 + - + +
47I ARG* 1.3 75.9 - - - +
49I TRP* 1.3 57.1 + - - +
51I LEU* 3.8 5.0 - - - +
52I SER* 3.0 27.0 + - - -
122I PHE 5.1 2.7 - - - -
125I LYS* 3.8 7.4 - - + +
126I LEU* 3.6 49.8 - - + +
129I ARG* 4.0 4.9 - - - +
417I LEU* 3.7 32.8 - - + +
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Residues in contact with TRP 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLN* 3.1 37.5 - - + -
39I LYS* 3.7 42.0 + - + +
40I ILE* 3.6 35.6 - - + +
41I PRO* 6.1 0.6 - - + +
44I THR* 4.5 13.0 - - + -
45I ASN 2.8 20.1 + - - +
46I ARG 3.7 3.4 - - - +
48I VAL* 1.3 72.3 - - - +
50I GLU* 1.3 78.1 + - + +
52I SER* 3.2 7.1 + - - -
53I LYS* 3.0 31.2 + - + +
305I GLN* 4.9 3.2 - - - +
417I LEU 5.0 1.3 - - - -
418I ASN* 3.2 34.6 + - + -
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLN* 5.5 5.2 + - - +
46I ARG* 3.0 32.3 + - + +
47I ARG* 4.1 3.4 - - - +
49I TRP* 1.3 88.8 - - + +
51I LEU* 1.3 62.5 + - - +
53I LYS* 3.4 6.2 + - - +
54I ALA 3.2 16.5 + - - -
57I ARG* 4.9 0.3 + - - -
111I ILE* 3.6 38.3 - - + +
122I PHE* 4.4 13.1 - - + -
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Residues in contact with LEU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ARG 3.3 16.1 + - - +
48I VAL 3.8 2.9 - - - +
50I GLU* 1.3 77.7 - - - +
52I SER* 1.3 56.3 + - - +
54I ALA* 3.1 5.2 + - - +
55I ASN* 2.8 48.9 + - - +
108I PHE* 3.9 16.8 - - + -
111I ILE* 3.7 13.3 - - + +
119I ILE* 4.5 3.4 - - + -
122I PHE* 3.5 42.1 - - + +
123I PHE* 3.5 28.3 - - + -
126I LEU* 3.6 28.7 - - + -
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Residues in contact with SER 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I VAL 3.0 19.7 + - - -
49I TRP* 3.2 7.3 + - - -
51I LEU* 1.3 76.1 - - - +
53I LYS* 1.3 53.9 + - - +
55I ASN* 3.4 9.8 + - - +
56I SER* 2.7 39.8 + - - -
126I LEU* 5.5 0.9 - - - +
417I LEU 3.7 10.3 - - - -
418I ASN* 2.8 41.3 + - - +
419I THR* 4.2 11.6 - - - -
901I GOL 4.7 0.5 + - - -
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Residues in contact with LYS 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I TRP* 3.0 21.7 + - + +
50I GLU* 3.6 11.0 - - - +
52I SER* 1.3 77.8 + - - +
54I ALA* 1.3 53.3 + - - +
56I SER* 3.1 8.1 + - - -
57I ARG* 2.8 58.4 + - + +
301I PRO* 5.5 0.3 - - - +
901I GOL 5.9 0.7 - - - -
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Residues in contact with ALA 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU 3.2 9.8 + - - +
51I LEU 3.1 10.0 + - - +
53I LYS* 1.3 76.2 - - - +
55I ASN* 1.3 62.2 + - - +
57I ARG* 3.0 29.1 + - - +
58I PHE* 3.1 10.7 + - - +
106I PHE 4.6 2.5 - - - -
107I LYS* 3.6 28.9 - - - +
108I PHE* 4.5 9.0 - - + -
110I THR* 4.0 2.0 - - - +
111I ILE* 3.8 19.7 - - + -
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Residues in contact with ASN 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 2.8 52.8 + - - +
52I SER* 3.6 8.2 - - - +
54I ALA* 1.3 72.8 - - - +
56I SER* 1.3 57.0 - - - +
58I PHE* 3.4 6.1 + - - +
59I ALA* 3.0 27.9 + - - +
80I PRO* 5.2 1.6 - - - +
81I LEU* 4.7 11.8 - - + +
84I SER* 3.3 33.3 + - - +
106I PHE 5.2 1.1 - - - +
108I PHE* 3.4 15.8 - - - -
123I PHE* 3.8 8.5 - - - -
126I LEU* 4.4 6.7 - - - +
419I THR* 6.1 3.3 - - - +
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Residues in contact with SER 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I SER 2.7 26.1 + - - -
53I LYS* 3.5 7.4 - - - -
55I ASN* 1.3 69.9 - - - +
57I ARG* 1.3 57.5 + - - +
59I ALA* 3.4 8.5 + - - +
60I THR* 2.7 35.4 + - - -
301I PRO* 4.7 7.9 - - - -
418I ASN 4.2 3.1 + - - -
419I THR* 4.9 0.2 - - - -
420I ILE* 3.2 32.1 + - - +
901I GOL 3.3 21.5 + - - -
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Residues in contact with ARG 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU 4.9 1.0 + - - -
53I LYS* 2.8 36.0 + - + +
54I ALA* 3.2 32.3 - - - +
56I SER* 1.3 71.9 - - - +
58I PHE* 1.3 66.4 + - - +
60I THR* 3.4 2.6 + - - -
61I THR* 3.1 24.8 + - - -
107I LYS* 3.6 24.5 - - + +
110I THR* 2.6 52.5 + - - +
111I ILE* 5.3 0.8 - - - +
301I PRO* 3.9 24.8 - - + +
302I GLU* 5.1 6.4 + - - -
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Residues in contact with PHE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ALA 3.1 8.1 + - - +
55I ASN* 3.6 8.3 - - - +
57I ARG* 1.3 76.4 - - - +
59I ALA* 1.3 67.5 + - - +
61I THR* 3.0 6.8 + - - -
62I PHE* 2.9 56.3 + + + +
80I PRO* 4.9 5.8 - - + -
83I ILE* 4.0 17.3 - - + -
84I SER* 3.5 19.5 - - - +
105I VAL* 3.4 29.2 - - + -
106I PHE* 3.4 48.0 - + - +
107I LYS* 3.8 6.1 - - - +
335I LEU* 4.1 5.8 - - + -
338I MET* 3.9 21.1 - - + -
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Residues in contact with ALA 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASN 3.0 17.7 + - - +
56I SER* 3.5 10.3 - - - +
58I PHE* 1.3 77.3 - - - +
60I THR* 1.3 66.1 + - - +
62I PHE* 4.3 2.1 - - - +
63I TYR* 3.1 24.4 + - - +
78I LEU* 5.9 0.5 - - - +
80I PRO* 3.5 34.7 - - + +
420I ILE* 4.5 12.1 - - + -
423I MET* 3.3 10.4 - - - +
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Residues in contact with THR 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I SER 2.7 18.7 + - - -
57I ARG 3.8 3.4 - - - -
58I PHE 3.2 0.4 + - - -
59I ALA* 1.3 75.1 - - - +
61I THR* 1.3 53.6 + - - +
63I TYR* 3.2 5.0 + - - +
64I GLN* 2.7 41.4 + - + +
299I LEU* 3.4 49.4 - - + +
300I THR* 4.1 2.7 - - - -
301I PRO* 3.5 28.9 - - + +
304I LEU* 5.3 8.2 - - + +
420I ILE* 5.5 0.7 - - - +
423I MET* 4.5 6.0 - - + +
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Residues in contact with THR 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ARG 3.1 12.2 + - - -
58I PHE* 3.0 10.2 + - - -
60I THR* 1.3 76.7 - - - +
62I PHE* 1.3 57.5 + - - +
64I GLN* 2.9 15.1 + - + +
65I HIS* 2.8 30.5 + - + +
107I LYS* 4.1 21.6 + - - -
338I MET* 3.6 22.7 - - + -
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Residues in contact with PHE 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PHE* 2.9 50.4 + + + +
59I ALA* 4.3 2.2 - - - +
61I THR* 1.3 72.0 - - - +
63I TYR* 1.3 54.4 + - - +
65I HIS* 3.2 2.8 + - - +
66I LEU* 2.7 54.1 + - + +
78I LEU* 4.1 17.0 - - + -
83I ILE* 4.3 10.1 - - + -
329I PHE* 5.5 2.7 - + - -
331I LEU* 3.5 29.4 - - + -
334I GLN* 3.3 39.6 + - + +
335I LEU* 4.1 23.6 - - + -
338I MET* 3.8 17.0 - - - +
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Residues in contact with TYR 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ALA 3.1 19.1 + - - +
60I THR 3.3 2.9 - - - +
62I PHE* 1.3 79.4 - - - +
64I GLN* 1.3 67.3 + - + +
66I LEU* 3.2 5.2 + - + +
67I ALA* 2.9 24.8 + - + +
76I ILE* 3.7 29.6 - - + -
78I LEU* 4.2 13.8 - - + +
296I GLU* 2.6 40.0 + - + -
299I LEU* 4.6 11.0 - - + -
409I LEU* 3.1 25.7 - - + +
423I MET* 3.6 36.3 - - + -
424I GLY* 3.4 16.9 + - - -
425I ARG* 3.4 11.6 + - - +
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Residues in contact with GLN 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I THR* 2.7 28.2 + - + +
61I THR* 2.9 18.3 + - + +
63I TYR* 1.3 76.7 - - + +
65I HIS* 1.3 62.0 + - - +
67I ALA* 3.4 6.4 + - - +
68I ASP* 3.2 22.7 + - - +
296I GLU* 3.0 20.1 + - - +
297I LYS* 2.9 30.9 + - - +
299I LEU* 3.4 21.1 + - + +
301I PRO* 6.0 0.2 - - - +
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Residues in contact with HIS 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I THR* 2.8 17.1 + - + +
62I PHE* 3.3 10.1 - - - +
64I GLN* 1.3 70.9 - - - +
66I LEU* 1.3 58.2 + - - +
68I ASP* 2.8 28.4 + - + +
69I SER* 3.1 18.0 + - - -
334I GLN* 3.5 32.9 - - + +
337I ASP* 3.5 29.2 + - + -
338I MET* 4.5 18.5 - - + +
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Residues in contact with LEU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I PHE* 2.7 34.9 + - + +
63I TYR* 3.7 4.7 - - + +
65I HIS* 1.3 70.8 - - - +
67I ALA* 1.3 60.0 + - - +
69I SER* 3.2 19.8 + - - +
70I LYS* 3.4 40.9 + - + +
76I ILE* 4.3 7.0 - - + -
78I LEU* 3.9 23.3 - - + -
329I PHE* 3.9 28.7 - - + -
334I GLN* 3.6 23.2 - - - +
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Residues in contact with ALA 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I TYR* 2.9 25.0 + - + +
64I GLN* 3.4 7.4 - - - +
66I LEU* 1.3 70.3 - - - +
68I ASP* 1.3 58.1 + - - +
70I LYS* 3.0 26.4 + - - +
72I ASP* 5.5 0.7 - - - +
76I ILE* 4.1 7.0 - - + +
296I GLU* 3.8 17.0 - - + +
425I ARG* 3.2 31.5 + - - +
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Residues in contact with ASP 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLN 3.2 9.5 + - - +
65I HIS* 2.8 22.3 + - + +
67I ALA* 1.3 75.2 - - - +
69I SER* 1.3 58.6 + - - +
70I LYS 3.1 6.1 + - - +
297I LYS* 5.2 12.2 - - - +
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Residues in contact with SER 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I HIS* 3.1 17.5 + - - -
66I LEU* 3.2 22.8 + - - +
68I ASP* 1.3 74.3 - - - +
70I LYS* 1.3 60.5 + - - +
334I GLN* 5.1 4.2 + - - -
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Residues in contact with LYS 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I LEU* 3.4 39.0 + - - +
67I ALA 3.0 18.8 + - - +
68I ASP 3.1 4.8 + - - +
69I SER* 1.3 83.6 - - - +
71I ASN* 1.3 69.4 + - - +
72I ASP* 3.9 5.7 + - - +
74I ASP* 4.5 11.0 - - + +
75I ASN 4.6 5.0 + - - +
76I ILE* 3.6 34.1 - - + +
327I ASP* 3.6 23.0 + - - -
329I PHE* 4.7 3.8 - - - -
425I ARG* 5.1 2.0 + - - +
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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