Contacts of the helix formed by residues 26 - 56 (chain A) in PDB entry 4YAY
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 TYR 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 3.6 28.0 - + + -
25A ASN* 1.3 79.6 - - + +
27A ILE* 1.3 81.3 + - + +
29A VAL* 3.3 6.0 + - - +
30A MET* 2.8 51.8 + - + +
282A THR* 3.3 20.8 + - - +
286A ILE* 4.9 11.9 - - + -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.4 21.5 - - - +
24A HIS* 3.3 21.4 + - + +
26A TYR* 1.3 87.6 - - + +
28A PHE* 1.3 62.0 + - + +
29A VAL 3.0 10.1 + - - -
30A MET* 4.5 3.1 - - + +
31A ILE* 3.3 37.4 + - + +
32A PRO* 3.7 0.9 - - - +
88A THR* 4.1 6.4 - - + +
92A TYR* 3.7 21.5 - - - +
282A THR* 3.1 39.3 - - - +
285A PRO* 3.8 15.9 - - + -
286A ILE* 5.1 4.5 - - + -
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.7 46.0 - - + -
24A HIS 3.4 26.2 - - - -
25A ASN* 3.7 12.3 + - - +
26A TYR 3.4 0.8 - - - -
27A ILE* 1.3 79.3 - - + +
29A VAL* 1.3 61.1 + - + +
32A PRO* 3.3 15.9 - - - +
88A THR* 3.2 26.0 - - + +
89A ALA* 3.5 15.1 - - - +
91A GLU* 3.6 42.8 - - + +
92A TYR* 3.6 26.9 - + - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.8 13.7 - - - +
26A TYR* 3.3 8.0 + - - +
27A ILE 3.0 0.2 - - - -
28A PHE* 1.3 85.0 - - + +
30A MET* 1.4 61.5 + - - +
31A ILE 3.6 0.7 - - - -
32A PRO* 3.5 4.4 - - - +
33A THR* 2.9 41.5 + - + +
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 2.8 36.8 + - + +
27A ILE* 4.4 2.9 - - - +
29A VAL* 1.4 71.2 - - - +
31A ILE* 1.3 75.1 + - + +
33A THR* 2.8 18.2 + - - -
34A LEU* 3.2 35.6 + - + +
286A ILE* 3.7 43.1 - - + -
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.3 30.4 + - + +
30A MET* 1.3 82.6 - - + +
32A PRO* 1.4 67.2 - - + +
34A LEU* 3.2 7.6 + - + +
35A TYR* 2.9 64.0 + - + +
88A THR* 3.9 17.3 - - + +
285A PRO* 3.5 30.5 - - + +
286A ILE* 3.9 20.2 - - + +
289A CYS* 4.7 7.6 - - + -
1201A ZD7 4.4 4.7 - - + -
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE 3.7 9.6 - - - +
28A PHE 3.3 21.8 - - - +
29A VAL* 3.5 12.8 - - - +
31A ILE* 1.4 92.6 - - + +
33A THR* 1.4 49.9 + - + +
35A TYR* 3.6 7.7 + - + +
36A SER* 2.6 36.3 + - - -
85A ALA* 3.4 31.3 - - + +
88A THR* 4.5 4.7 - - - -
89A ALA* 3.8 15.3 - - + -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 2.9 25.5 + - + +
30A MET* 2.8 24.3 + - - -
32A PRO* 1.4 76.5 - - + +
34A LEU* 1.4 64.4 + - - +
36A SER* 3.4 19.3 - - - -
37A ILE* 3.5 19.9 - - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.2 43.5 + - + +
31A ILE* 3.2 9.8 + - + +
33A THR* 1.4 77.9 + - - +
35A TYR* 1.4 59.7 + - - +
37A ILE* 3.4 14.4 + - + +
38A ILE* 3.1 31.0 + - + +
286A ILE* 6.3 2.2 - - + -
289A CYS* 3.6 29.8 - - - -
290A ILE* 6.5 0.7 - - + -
293A PHE* 4.5 14.5 - - + -
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 2.9 37.4 + - + +
32A PRO 3.9 0.7 - - - +
34A LEU* 1.4 75.7 - - - +
36A SER* 1.3 59.6 + - - +
37A ILE 3.3 0.2 - - - -
38A ILE* 4.2 7.6 - - + +
39A PHE* 3.1 26.3 + - - +
81A LEU* 3.3 37.1 - - + +
82A PRO* 6.2 0.2 - - - +
84A TRP* 4.2 4.7 - - + -
85A ALA* 3.8 36.8 - - + -
285A PRO 4.1 0.3 + - - -
288A ILE* 3.8 11.3 - - - +
289A CYS* 3.7 33.7 - - + -
292A TYR* 6.5 0.2 - - + -
1201A ZD7 3.0 54.0 + - + +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO 2.6 21.9 + - - -
33A THR* 3.4 11.8 - - - -
34A LEU 3.3 0.2 - - - -
35A TYR* 1.3 77.5 - - - +
37A ILE* 1.3 58.6 + - - +
39A PHE* 3.6 5.3 + - - +
40A VAL* 3.1 36.9 + - - +
85A ALA* 5.3 2.4 - - - +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 3.5 22.0 - - - +
34A LEU* 3.4 15.2 + - + +
35A TYR 3.3 0.4 - - - -
36A SER* 1.3 74.8 - - - +
38A ILE* 1.4 68.5 + - + +
39A PHE 3.3 0.2 + - - -
40A VAL* 3.4 2.2 + - - -
41A VAL* 2.8 47.6 + - + +
293A PHE* 6.2 3.8 - - + -
296A CYS* 6.0 2.2 - - - -
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 3.1 17.3 + - - +
35A TYR* 4.2 11.4 - - + -
36A SER 3.6 0.2 - - - -
37A ILE* 1.4 73.5 - - + +
39A PHE* 1.4 58.0 + - - +
42A GLY* 2.9 27.4 + - - -
77A PHE* 5.3 1.6 - - + -
78A LEU* 3.5 10.4 - - + +
81A LEU* 3.7 19.5 - - + -
289A CYS* 3.8 25.4 - - - +
292A TYR* 4.4 15.3 - - + +
293A PHE* 3.7 34.8 - - + +
295A ASN* 5.0 0.2 - - + -
296A CYS* 3.3 39.0 - - + +
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR 3.1 19.2 + - - +
36A SER* 3.8 4.7 - - - +
37A ILE 3.3 0.2 - - - -
38A ILE* 1.4 76.3 - - - +
40A VAL* 1.4 70.0 + - + +
43A ILE* 2.9 60.6 + - + +
78A LEU* 3.1 38.4 - - - +
79A LEU* 4.4 10.1 - - + -
81A LEU* 3.6 9.1 - - + +
82A PRO* 3.7 28.7 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.1 19.9 + - - +
37A ILE* 4.2 2.7 - - - +
39A PHE* 1.4 87.4 - - + +
41A VAL* 1.3 71.9 + - + +
43A ILE* 4.0 3.2 - - - +
44A PHE* 3.4 34.5 + - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 2.8 41.6 + - + +
38A ILE 4.4 0.4 - - - +
40A VAL* 1.3 74.7 - - + +
42A GLY* 1.3 55.8 + - - +
44A PHE* 3.6 3.6 + - - +
45A GLY* 2.9 27.6 + - - -
296A CYS* 4.0 23.6 - - + +
300A LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE 2.9 20.4 + - - -
41A VAL* 1.3 75.5 - - - +
43A ILE* 1.4 58.1 + - - +
45A GLY* 4.4 0.9 - - - -
46A ASN* 2.9 35.8 + - - +
78A LEU* 3.4 12.4 - - - +
295A ASN 4.1 0.9 - - - -
296A CYS* 3.7 21.9 - - - +
299A PRO* 5.0 0.4 - - - -
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 2.9 50.8 + - + +
40A VAL* 4.0 4.7 - - - +
41A VAL 3.4 0.4 - - - -
42A GLY* 1.4 71.1 - - - +
44A PHE* 1.4 66.4 + - + +
47A SER* 2.7 37.2 + - - +
75A LEU* 3.8 20.8 - - + +
78A LEU* 3.8 21.3 - - + -
79A LEU* 4.2 24.5 - - + -
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.4 25.9 + - + +
41A VAL* 4.1 3.1 - - - +
43A ILE* 1.4 84.8 - - + +
45A GLY* 1.3 64.2 + - - +
47A SER* 3.1 16.6 + - - -
48A LEU* 3.2 29.9 + - + +
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 2.9 18.6 + - - -
43A ILE 3.3 0.2 - - - -
44A PHE* 1.3 76.1 - - - +
46A ASN* 1.3 61.4 + - - +
48A LEU* 3.3 10.7 + - - +
49A VAL* 3.3 22.7 + - - +
299A PRO* 3.4 21.9 - - - +
300A LEU* 6.1 1.6 - - - -
----------------------------------------------------------
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 2.9 24.4 + - - +
45A GLY* 1.3 69.5 - - - -
47A SER* 1.3 63.9 + - - +
49A VAL* 3.3 10.3 + - - +
50A VAL* 3.2 26.9 + - - +
71A ALA* 4.0 21.5 - - + +
74A ASP* 3.8 17.9 - - - +
75A LEU* 3.6 15.3 - - + -
78A LEU* 3.5 10.9 - - - +
295A ASN 2.7 28.3 + - - +
298A ASN* 4.8 1.6 - - - +
299A PRO* 3.4 20.2 - - - +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 2.7 29.0 + - - +
44A PHE* 3.1 14.7 + - - -
46A ASN* 1.3 76.3 - - - +
48A LEU* 1.4 60.3 + - - +
50A VAL* 3.4 11.1 + - - +
51A ILE* 3.3 26.8 + - - +
75A LEU* 4.2 10.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.2 32.7 + - + +
45A GLY* 3.5 7.9 - - - +
46A ASN 3.3 0.2 - - - -
47A SER* 1.4 75.5 + - - +
49A VAL* 1.4 58.4 + - + +
51A ILE* 3.3 13.7 + - + +
52A VAL* 3.0 36.6 + - + +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 3.3 14.9 + - - +
46A ASN* 3.4 13.2 - - - +
48A LEU* 1.4 74.1 - - + +
50A VAL* 1.4 58.2 + - - +
52A VAL* 3.3 8.0 + - - +
53A ILE* 2.9 51.1 + - + +
71A ALA* 4.0 15.5 - - + -
299A PRO* 3.7 28.3 - - + +
302A TYR* 3.7 34.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN 3.2 16.5 + - - +
47A SER* 3.6 10.5 - - - +
48A LEU 3.4 0.2 - - - -
49A VAL* 1.4 74.6 - - - +
51A ILE* 1.4 65.7 + - + +
53A ILE* 3.5 1.9 + - - +
54A TYR* 3.2 39.0 + - + -
68A LEU* 3.9 24.5 - - + -
71A ALA* 3.9 19.1 - - + -
72A LEU* 4.6 17.9 - - + -
75A LEU* 4.9 8.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 3.3 16.1 + - - +
48A LEU* 3.3 17.5 + - + +
50A VAL* 1.4 79.6 - - + +
52A VAL* 1.4 61.0 + - + +
54A TYR* 3.3 3.9 + - + -
55A PHE* 3.0 60.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.0 25.1 + - + +
49A VAL* 3.3 8.7 + - - +
51A ILE* 1.4 76.5 - - + +
53A ILE* 1.4 59.3 + - + +
55A PHE* 5.2 0.7 - - - -
56A TYR* 2.7 54.1 + - + +
57A MET* 3.1 17.1 + - + -
302A TYR* 5.3 9.6 - - + -
309A PHE* 4.1 26.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.9 39.5 + - + +
50A VAL* 3.9 4.0 - - - +
51A ILE 3.4 0.2 - - - -
52A VAL* 1.4 74.3 - - + +
54A TYR* 1.3 58.3 + - - +
57A MET* 3.4 28.3 - - + +
58A LYS 2.8 23.7 + - - -
59A LEU* 3.4 19.9 + - + -
64A SER* 3.4 26.7 - - - +
67A LEU* 3.7 12.6 - - + +
68A LEU* 3.6 41.1 - - + +
302A TYR* 4.2 3.4 - - + +
----------------------------------------------------------
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.2 37.1 + - + +
51A ILE* 3.3 5.6 + - + +
53A ILE* 1.3 78.9 - - - +
55A PHE* 1.4 70.5 + - + +
58A LYS* 3.3 22.0 + - - +
59A LEU* 3.6 25.1 - - + +
68A LEU* 4.0 27.0 - - + +
----------------------------------------------------------
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.0 48.8 + - + +
52A VAL* 5.2 0.7 - - - -
54A TYR* 1.4 91.0 - - + +
56A TYR* 1.3 61.1 + - - +
58A LYS* 3.3 30.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.7 35.5 + - + +
55A PHE* 1.3 75.9 - - - +
57A MET* 1.3 77.3 + - + +
58A LYS* 4.9 1.9 - - - +
305A LEU* 4.6 17.8 + - + +
308A LYS* 3.4 33.4 + - - +
309A PHE* 4.0 28.7 - + + -
312A TYR* 3.9 29.8 - - + -
----------------------------------------------------------
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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