Contacts of the helix formed by residues 25 - 60 (chain A) in PDB entry 5DSG
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 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER 3.6 3.4 + - - +
24A HIS* 1.3 77.0 - - - +
26A ARG* 1.3 67.1 + - + +
27A TYR* 3.1 16.9 + - + +
28A GLU* 2.9 40.7 + - - +
29A THR* 3.1 20.9 + - - -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 1.3 73.8 - - + +
27A TYR* 1.3 106.6 + - + +
29A THR* 3.3 6.3 + - - -
30A VAL* 2.9 39.6 + - + +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.1 11.7 + - + +
26A ARG* 1.3 119.3 + - + +
28A GLU* 1.3 57.5 + - - +
30A VAL* 4.0 4.8 - - - +
31A GLU* 2.9 36.6 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 4.3 26.9 + - + +
25A ASN* 2.9 33.6 + - - +
27A TYR* 1.3 77.3 - - - +
29A THR* 1.3 56.6 + - - +
31A GLU* 3.7 9.6 - - - +
32A MET* 2.9 71.1 + - + +
94A ILE 4.5 3.5 - - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 3.7 20.8 + - - +
25A ASN 3.1 12.5 + - - -
26A ARG* 3.3 10.1 + - - -
28A GLU* 1.3 79.9 - - - +
30A VAL* 1.3 60.2 + - + +
32A MET* 3.9 3.4 - - - +
33A VAL* 2.9 48.3 + - + +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.9 25.3 + - + +
27A TYR* 4.0 4.5 - - - +
29A THR* 1.3 77.7 - - + +
31A GLU* 1.3 58.8 + - - +
33A VAL* 3.9 5.0 - - - +
34A PHE* 2.9 33.1 + - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 2.9 23.1 + - - +
28A GLU* 3.7 13.4 - - - +
30A VAL* 1.3 78.4 - - - +
32A MET* 1.3 76.2 + - + +
34A PHE* 3.6 6.5 - - + +
35A ILE* 2.9 52.2 + - + +
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 6.2 2.2 - - + +
28A GLU* 2.9 52.0 + - + +
29A THR* 4.0 3.6 - - - +
31A GLU* 1.3 93.6 - - - +
33A VAL* 1.3 61.8 + - + +
35A ILE* 3.9 13.9 - - + +
36A ALA* 2.9 31.2 + - - +
93A ILE* 4.1 7.6 - - + +
94A ILE* 3.6 56.4 - - + +
96A GLY* 6.1 0.9 - - - -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 2.9 35.6 + - + +
30A VAL* 3.9 4.9 - - - +
32A MET* 1.3 74.3 - - + +
34A PHE* 1.3 59.8 + - - +
36A ALA* 3.9 4.9 - - - +
37A THR* 2.7 46.2 + - - +
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 2.9 22.7 + - + +
31A GLU* 3.6 8.1 - - + +
33A VAL* 1.3 77.8 - - - +
35A ILE* 1.3 65.9 + - + +
37A THR* 3.3 5.7 + - - -
38A VAL* 2.9 61.0 + - + +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 2.9 44.1 + - + +
32A MET* 3.9 13.2 - - - +
34A PHE* 1.3 86.7 - - + +
36A ALA* 1.3 52.2 + - - +
38A VAL* 4.8 2.0 - - - -
39A THR* 2.6 57.0 + - + +
90A THR* 5.3 2.2 - - + -
93A ILE* 4.0 31.0 - - + -
94A ILE* 4.3 16.2 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET 2.9 20.1 + - - +
33A VAL* 3.9 5.4 - - - +
35A ILE* 1.3 76.8 - - - +
37A THR* 1.3 59.5 + - - +
39A THR* 3.5 5.3 + - - -
40A GLY* 2.9 27.4 + - - -
94A ILE* 3.9 19.3 - - + -
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 2.7 31.5 + - - +
34A PHE* 3.6 6.0 - - - -
36A ALA* 1.3 75.0 - - - +
38A VAL* 1.3 61.5 + - + +
40A GLY* 3.9 0.2 - - - -
41A SER* 2.7 43.9 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 2.9 53.1 + - + +
35A ILE* 4.0 3.4 - - - +
37A THR* 1.3 77.9 - - + +
39A THR* 1.3 64.1 + - + +
41A SER* 3.2 7.3 + - - -
42A LEU* 2.9 46.1 + - + +
440A TRP* 5.7 1.1 - - - +
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 2.6 38.6 + - + +
36A ALA* 3.5 6.4 + - - -
38A VAL* 1.3 76.5 - - + +
40A GLY* 1.3 62.1 + - - +
42A LEU* 3.4 2.9 + - - +
43A SER* 2.9 27.9 + - - -
86A MET* 5.2 0.3 - - - +
87A ASN* 5.8 0.4 - - - -
90A THR* 3.4 31.6 - - + +
93A ILE* 5.8 2.7 - - + -
440A TRP* 3.5 40.2 - - + +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 2.9 19.9 + - - -
37A THR 3.9 0.2 - - - -
39A THR* 1.3 74.1 + - - +
41A SER* 1.3 59.2 + - - +
43A SER* 3.2 7.6 + - - -
44A LEU* 2.9 29.0 + - - +
87A ASN* 5.2 4.5 - - - -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 2.7 29.7 + - - +
38A VAL* 3.4 6.7 - - - -
40A GLY* 1.3 76.3 - - - +
42A LEU* 1.3 58.6 + - - +
44A LEU* 3.3 8.0 + - - +
45A VAL* 2.9 38.5 + - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 2.9 35.3 + - + +
39A THR* 3.7 4.9 - - - +
41A SER* 1.3 77.6 - - - +
43A SER* 1.3 54.6 + - - +
45A VAL* 3.8 5.9 - - + +
46A THR* 2.5 39.6 + - - -
86A MET* 4.1 4.7 - - + -
440A TRP* 3.9 32.8 - - + +
444A VAL* 5.1 17.3 - - + -
447A THR* 3.8 20.7 + - + +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 2.9 14.5 + - - -
40A GLY* 3.3 10.5 - - - -
42A LEU* 1.3 76.7 - - - +
44A LEU* 1.3 57.5 + - - +
46A THR* 3.2 2.4 + - - -
47A VAL* 2.9 37.4 + - - +
82A GLY 2.9 18.9 + - - -
86A MET* 3.7 17.0 - - - -
87A ASN* 3.4 28.2 + - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 2.9 15.8 + - - +
41A SER* 3.7 6.1 - - - +
43A SER* 1.3 75.9 + - - +
45A VAL* 1.3 60.6 + - + +
47A VAL* 3.8 6.6 - - + +
48A VAL* 2.9 53.6 + - + +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 2.9 24.5 + - - +
42A LEU* 3.8 8.5 - - + +
44A LEU* 1.3 77.8 - - + +
46A THR* 1.3 58.5 + - - +
48A VAL* 4.2 3.5 - - - +
49A GLY* 2.9 27.9 + - - -
447A THR* 3.7 22.6 - - + +
450A PRO* 5.6 0.5 - - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 2.5 19.3 + - - -
43A SER 3.2 4.2 + - - -
45A VAL* 1.3 77.3 - - - +
47A VAL* 1.3 63.0 + - - +
49A GLY* 3.8 0.6 - - - -
50A ASN* 2.8 47.6 + - - +
78A ASP 3.6 16.4 - - - +
82A GLY* 3.7 16.6 - - - -
86A MET* 3.5 4.9 - - + +
446A SER* 3.6 19.3 - - - +
447A THR* 2.3 36.0 + - - +
450A PRO* 5.6 0.4 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 2.9 24.1 + - - +
44A LEU* 3.8 8.1 - - + +
46A THR* 1.3 76.1 - - - +
48A VAL* 1.3 67.0 + - + +
51A ILE* 2.9 48.2 + - + +
79A LEU* 3.8 18.2 - - + +
82A GLY 3.8 23.8 - - - +
83A ALA* 3.9 15.9 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.9 42.4 + - + +
45A VAL* 4.2 3.6 - - - +
47A VAL* 1.3 80.3 - - + +
49A GLY* 1.3 57.6 + - - +
51A ILE* 3.4 7.5 + - + +
52A LEU* 2.9 46.7 + - + +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL 2.9 19.7 + - - -
46A THR 3.8 0.4 - - - -
48A VAL* 1.3 78.8 - - - +
50A ASN* 1.3 55.5 + - - +
52A LEU* 3.1 13.5 + - - +
53A VAL* 2.9 29.1 + - - +
450A PRO* 3.8 20.1 - - - +
464A PHE* 4.7 0.7 - - - -
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 2.8 37.8 + - - +
47A VAL 4.1 0.4 - - - +
49A GLY* 1.3 72.4 - - - +
51A ILE* 1.3 60.9 + - - +
53A VAL* 3.5 6.5 - - - +
54A MET* 2.9 35.9 + - - +
75A ALA* 3.5 24.9 - - - +
78A ASP* 3.1 29.9 - - - +
79A LEU* 4.0 11.2 - - + +
446A SER 3.2 21.8 + - - -
449A ASN* 5.1 0.9 - - - +
450A PRO* 3.6 15.3 - - - +
453A TYR* 5.5 1.2 - - - -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 2.9 39.4 + - + +
48A VAL* 3.6 9.2 - - + +
50A ASN* 1.3 77.4 - - - +
52A LEU* 1.3 58.6 + - + +
54A MET* 3.4 7.8 + - - +
55A LEU* 2.9 49.2 + - + +
79A LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.9 35.0 + - + +
49A GLY* 3.1 12.3 + - - +
51A ILE* 1.3 79.4 - - + +
53A VAL* 1.3 52.3 + - - +
55A LEU* 4.5 9.2 - - + -
56A SER* 2.6 37.6 + - - -
464A PHE* 3.4 23.6 - - + -
467A LEU* 3.7 20.4 - - + +
468A LEU* 3.7 35.2 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 2.9 20.2 + - - +
50A ASN* 3.2 9.8 + - - +
52A LEU* 1.3 75.9 - - - +
54A MET* 1.3 64.5 + - - +
56A SER* 3.1 5.7 + - - -
57A ILE* 2.9 31.1 + - + +
71A LEU 4.9 0.4 - - - +
75A ALA* 4.0 15.0 - - + -
450A PRO* 3.8 11.4 - - + -
453A TYR* 3.6 42.0 - - + -
460A PHE* 4.3 13.5 - - + -
464A PHE* 3.7 20.2 - - + -
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN 2.9 22.1 + - - +
51A ILE* 3.8 6.5 - - - +
53A VAL* 1.3 76.2 - - - +
55A LEU* 1.3 59.6 + - + +
57A ILE* 3.2 4.9 + - - +
58A LYS* 2.9 32.3 + - - +
72A PHE* 3.5 34.0 - - + +
75A ALA* 3.8 27.8 - - + +
76A CYS* 3.7 24.7 - - - -
79A LEU* 3.9 29.2 - - + -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 2.9 38.7 + - + +
52A LEU* 3.8 7.6 - - + +
54A MET* 1.3 77.1 - - + +
56A SER* 1.3 57.0 + - - +
58A LYS* 3.1 11.4 + - + +
59A VAL* 2.9 40.2 + - + +
467A LEU* 3.7 25.6 - - + -
----------------------------------------------------------
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 2.6 25.6 + - - -
53A VAL 3.1 6.5 + - - -
55A LEU* 1.3 76.8 - - - +
57A ILE* 1.3 62.2 + - - +
59A VAL 4.7 0.2 - - - +
60A ASN* 3.1 30.5 + - - +
63A LEU* 4.0 3.4 - - - +
460A PHE* 4.1 13.7 - - - -
463A THR* 3.6 24.2 - - - +
464A PHE* 3.1 25.3 - - - -
467A LEU* 3.4 8.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 2.9 22.8 + - + +
54A MET 3.2 6.0 + - - +
56A SER* 1.3 76.5 - - - +
58A LYS* 1.3 62.6 + - - +
60A ASN 3.6 2.6 - - - +
63A LEU* 3.6 22.0 - - - +
64A GLN* 3.4 20.8 + - - +
68A ASN* 3.3 30.7 - - + +
71A LEU* 4.2 6.7 - - + -
72A PHE* 3.7 29.4 - - + +
460A PHE* 3.9 18.4 - - + -
1206A OLC 3.8 27.9 + - - -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET 2.9 10.5 + - - +
55A LEU* 3.1 18.4 + - + +
57A ILE* 1.3 79.2 - - - +
59A VAL* 1.3 62.2 + - + +
64A GLN* 3.2 18.3 + - - +
72A PHE* 3.5 39.0 - - + -
1206A OLC 2.9 33.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 2.9 25.2 + - + +
56A SER* 4.6 1.8 - - - +
58A LYS* 1.3 80.9 - - + +
60A ASN* 1.3 64.5 + - - +
61A ARG* 3.5 3.1 + - - +
64A GLN* 4.8 1.1 + - - -
463A THR* 5.4 3.4 - - + -
467A LEU* 4.2 24.5 - - + -
----------------------------------------------------------
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 3.1 17.8 + - - +
57A ILE 3.6 3.6 - - - +
59A VAL* 1.3 76.7 - - - +
61A ARG* 1.3 63.1 + - - +
62A GLN* 2.9 33.0 + - - +
63A LEU* 3.2 19.9 + - + +
64A GLN* 3.3 17.3 - - - +
459A THR* 3.4 23.6 - - - +
463A THR* 3.4 27.8 + - + +
----------------------------------------------------------
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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