Contacts of the helix formed by residues 43 - 76 (chain A) in PDB entry 5D0Y
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 LEU 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 34.9 - - + +
30A GLY* 5.4 0.2 - - - -
32A PHE* 3.1 37.8 + - + +
42A GLY* 1.3 73.6 - - - -
44A GLY* 1.3 64.3 + - - +
45A PHE* 3.2 13.9 - - + -
46A ILE* 3.1 42.1 + - + +
47A GLY 3.9 0.2 + - - -
159A VAL* 6.2 0.4 - - + -
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.8 22.7 + - - +
29A LEU* 3.9 3.4 + - - -
30A GLY* 3.9 22.2 - - - -
42A GLY 3.3 3.8 - - - -
43A LEU* 1.3 75.5 - - - +
45A PHE* 1.3 65.4 + - - +
46A ILE 3.1 0.5 + - - -
47A GLY* 3.3 4.2 + - - -
48A SER 3.2 15.4 + - - -
92A GLU* 5.1 0.7 - - - -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 3.2 24.4 + - - -
43A LEU* 4.0 10.3 - - + -
44A GLY* 1.3 76.6 - - - +
46A ILE* 1.3 86.2 + - + +
48A SER* 3.0 11.5 + - - +
49A VAL* 2.9 42.6 + - + +
92A GLU* 4.0 5.3 + - - +
96A TYR* 4.7 5.6 - - - +
122A TYR* 3.9 20.9 - - - +
155A ILE* 5.6 2.2 - - + -
156A HIS* 3.4 47.1 - + + +
159A VAL* 3.6 33.0 - - + -
160A VAL* 4.7 4.7 - - + -
201A FOL 5.3 3.8 - - - +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.9 20.0 - - + -
43A LEU* 3.3 44.4 - - + +
44A GLY 3.1 0.6 - - - -
45A PHE* 1.3 104.2 - - + +
47A GLY* 1.3 62.9 + - - +
49A VAL* 3.5 4.6 + - - +
50A MET* 3.2 29.4 + - - +
159A VAL* 4.1 11.7 - - + -
163A ILE* 3.7 29.2 - - + +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.5 2.6 - - - +
25A ILE* 4.7 0.7 - - - -
26A LYS* 3.4 33.2 - - - +
29A LEU* 4.3 5.6 - - - +
43A LEU 3.9 2.0 + - - -
44A GLY 3.3 3.6 + - - -
45A PHE 3.2 0.4 - - - -
46A ILE* 1.3 82.1 - - - +
48A SER* 1.3 60.6 + - - +
50A MET* 3.1 24.9 + - - +
51A LEU* 3.1 13.2 + - - +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.5 28.3 - - - +
44A GLY 3.2 6.2 + - - -
45A PHE* 3.0 15.3 + - - -
47A GLY* 1.3 75.2 - - - +
49A VAL* 1.3 60.4 + - - +
51A LEU* 3.5 0.6 + - - -
52A GLY* 3.4 11.3 + - - -
89A ALA 5.1 0.2 - - - -
92A GLU* 3.4 30.4 - - - +
93A SER* 2.5 38.6 + - - -
96A TYR* 3.9 7.4 - - - -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 2.9 26.4 + - + +
46A ILE* 3.8 5.6 - - - +
48A SER* 1.3 75.6 - - - +
50A MET* 1.3 59.2 + - - +
52A GLY* 3.1 2.8 + - - -
53A TYR* 2.8 28.1 + - + +
96A TYR* 3.5 50.5 - - + +
100A LEU* 4.3 6.5 - - + -
160A VAL* 4.0 18.2 - - + -
163A ILE* 4.7 8.5 - - + -
164A LEU* 4.2 25.1 - - + -
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.6 25.6 - - + -
25A ILE* 3.8 35.9 - - + -
29A LEU* 5.4 0.4 - - - -
46A ILE* 3.2 23.5 + - - +
47A GLY* 3.1 8.5 + - - +
49A VAL* 1.3 77.7 - - - +
51A LEU* 1.3 56.9 + - - +
53A TYR* 4.4 5.4 - - - +
54A LEU* 2.9 47.0 + - + +
163A ILE* 4.6 13.2 - - + -
167A LEU* 4.2 29.2 - - + -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.2 8.3 - - + -
22A VAL* 3.6 30.9 - - + +
23A ILE* 3.6 15.9 - - + -
26A LYS* 4.7 12.6 - - + -
47A GLY 3.1 12.2 + - - +
48A SER 3.6 0.7 - - - +
49A VAL 3.2 0.2 - - - -
50A MET* 1.3 75.0 - - - +
52A GLY* 1.3 58.1 + - - +
55A PHE* 3.3 41.0 + - + +
56A GLY 3.5 6.6 - - - +
59A TRP 4.7 4.3 - - - +
60A GLY* 3.8 6.1 - - - +
63A GLY* 3.3 35.2 - - - +
64A GLY* 3.3 7.6 - - - +
93A SER* 3.3 22.2 - - - +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 3.4 5.9 + - - -
49A VAL 3.1 6.3 + - - -
51A LEU* 1.3 77.0 - - - +
53A TYR* 1.3 65.6 + - - +
56A GLY 3.6 12.3 + - - -
93A SER 3.4 19.9 + - - -
96A TYR 4.1 5.2 - - - -
97A GLY* 3.5 28.8 - - - -
101A TYR* 3.6 7.6 - - - +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.8 17.2 + - + +
50A MET* 3.8 5.8 - - - +
52A GLY* 1.3 76.6 - - - +
54A LEU* 1.3 81.8 + - + +
96A TYR 4.7 0.6 + - - -
100A LEU* 3.4 32.5 - - + +
101A TYR* 3.1 24.6 - - - -
102A LYS 4.5 3.7 + - - -
103A LYS 4.4 13.2 + - - -
105A ILE* 3.8 15.2 - - + +
163A ILE* 6.1 2.9 - - + -
164A LEU* 4.0 48.6 + - + -
167A LEU* 4.6 23.0 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.9 14.8 - - + -
22A VAL* 5.0 3.4 - - + -
50A MET* 2.9 36.4 + - + +
53A TYR* 1.3 99.4 - - + +
55A PHE* 1.3 83.4 + - + +
101A TYR* 3.5 15.5 + - - -
167A LEU* 4.5 22.7 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.5 31.6 - - + -
16A LEU* 5.8 0.7 - - + -
18A LEU* 3.7 16.2 - - + -
19A LEU* 3.5 38.6 - - + -
22A VAL* 3.7 21.8 - - + -
51A LEU* 3.3 28.3 + - + +
54A LEU* 1.3 100.7 - - + +
56A GLY* 1.3 62.8 + - - +
59A TRP* 3.5 41.4 - - + +
60A GLY* 4.9 0.2 - - - -
101A TYR* 4.1 8.3 + - - -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 3.5 3.5 + - - +
52A GLY* 3.6 16.4 + - - -
55A PHE* 1.3 79.0 - - - +
57A PRO* 1.3 71.0 - - - +
58A TRP 3.6 0.7 - - - -
60A GLY* 2.9 26.7 + - - -
97A GLY* 4.4 1.8 - - - -
101A TYR* 3.5 25.9 - - - -
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 1.3 83.2 - - - +
58A TRP* 1.3 82.2 + - + +
61A PHE* 2.5 37.2 + - - +
94A MET* 3.3 29.6 - - + +
97A GLY* 4.2 8.5 - - - -
98A PHE* 3.5 37.5 - - + +
101A TYR* 4.2 13.0 - - + -
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Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 3.6 0.2 - - - -
57A PRO* 1.3 94.2 - - + +
59A TRP* 1.3 77.5 + + + +
61A PHE* 3.1 8.6 + - + +
62A ALA* 2.9 28.5 + - - +
94A MET* 4.8 11.2 - - - -
98A PHE* 4.1 31.2 - + - -
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Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 5.2 12.1 - - + -
19A LEU* 4.6 22.4 - - + +
51A LEU* 4.7 2.8 - - - +
55A PHE* 3.5 38.7 - + + +
56A GLY 4.2 0.4 + - - -
58A TRP* 1.3 93.3 - + + +
60A GLY* 1.3 56.9 + - - +
62A ALA* 3.6 10.3 - - + +
63A GLY* 2.9 24.4 + - - -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.8 20.2 + - - +
56A GLY 2.9 23.9 + - - -
57A PRO 3.4 0.9 - - - -
58A TRP 3.0 0.2 - - - -
59A TRP* 1.3 77.9 - - - +
61A PHE* 1.3 58.9 + - - +
62A ALA 3.3 0.2 - - - -
63A GLY* 4.1 0.4 - - - -
64A GLY 3.0 21.8 + - - -
93A SER* 3.1 24.4 - - - -
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 2.5 21.0 + - - +
58A TRP* 3.5 7.9 - + + +
60A GLY* 1.3 70.1 - - - +
62A ALA* 1.3 63.4 + - - +
65A ALA* 2.9 33.3 + - + +
87A LEU* 4.1 15.9 - - + -
90A ALA* 3.3 45.7 - - + +
91A LEU* 3.7 22.4 - - + -
94A MET* 3.8 22.6 - - + +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.2 1.8 - - + -
58A TRP 2.9 15.3 + - - +
59A TRP* 3.6 14.6 - - + +
61A PHE* 1.3 80.6 - - - +
63A GLY* 1.3 58.0 + - - +
65A ALA* 3.2 7.2 + - - +
66A LEU* 2.8 32.7 + - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.3 8.9 - - - +
23A ILE* 3.2 27.2 - - - +
51A LEU* 3.3 11.4 - - - +
59A TRP 2.9 21.1 + - - -
62A ALA* 1.3 74.1 - - - +
64A GLY* 1.3 55.3 + - - +
66A LEU* 4.2 4.5 - - - -
67A SER* 2.8 26.0 + - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 4.9 2.5 - - - -
51A LEU* 3.3 9.5 - - - +
60A GLY 3.0 16.5 + - - -
61A PHE 4.0 0.2 - - - -
63A GLY* 1.3 72.1 - - - +
65A ALA* 1.3 67.8 + - - +
66A LEU 3.2 0.5 + - - -
67A SER* 3.4 6.3 + - - -
68A ASP* 3.2 21.7 + - - +
89A ALA* 3.4 28.4 - - - +
93A SER* 4.3 2.0 - - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 2.9 27.1 + - + +
62A ALA* 3.5 6.5 - - - +
64A GLY* 1.3 76.0 - - - +
66A LEU* 1.3 63.1 + - - +
68A ASP* 3.5 9.0 + - - +
69A LEU* 3.5 19.0 + - + +
86A THR* 3.7 19.3 - - + +
90A ALA* 3.7 17.6 - - + +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.2 1.8 - - + -
23A ILE* 5.2 11.7 - - + -
62A ALA 2.8 18.2 + - - +
63A GLY* 3.7 7.9 - - - +
65A ALA* 1.3 72.9 - - - +
67A SER* 1.3 59.4 + - - +
68A ASP 3.0 4.3 - - - -
69A LEU* 2.8 42.9 + - + +
70A VAL* 3.1 21.7 + - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.4 32.9 - - - +
26A LYS* 3.3 29.6 + - - +
27A VAL* 3.2 12.7 - - - +
63A GLY 2.8 19.9 + - - -
64A GLY 3.4 7.8 + - - -
66A LEU* 1.3 72.7 - - - +
68A ASP* 1.3 59.9 + - - +
70A VAL* 4.0 2.5 - - - -
71A SER* 3.1 28.4 + - - -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 3.2 7.9 + - - +
65A ALA 3.6 10.3 - - - +
66A LEU 2.9 1.0 + - - -
67A SER* 1.3 81.0 + - - +
69A LEU* 1.3 58.7 + - - +
71A SER* 3.3 5.4 + - - -
72A SER* 2.8 35.0 + - - -
77A ASN* 5.5 0.2 + - - -
81A PHE* 4.3 1.0 - - - -
85A PHE 4.1 4.5 - - - +
86A THR* 2.7 35.9 + - - -
89A ALA* 4.1 14.0 - - + +
201A FOL 3.0 39.5 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.5 18.4 + - + +
66A LEU* 2.8 33.0 + - + +
68A ASP* 1.3 73.4 - - - +
70A VAL* 1.3 52.3 + - + +
72A SER* 3.2 7.3 + - - -
73A ALA* 2.8 36.6 + - - +
81A PHE* 4.3 24.2 - - + -
83A ILE* 5.9 2.0 - - + -
86A THR* 4.7 9.6 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 5.0 6.7 - - + -
27A VAL* 4.1 17.0 - - + -
66A LEU* 3.1 26.3 + - + +
67A SER* 4.1 5.2 - - - +
69A LEU* 1.3 78.1 - - + +
71A SER* 1.3 57.7 + - - +
73A ALA* 3.1 6.5 + - - +
74A ILE* 2.9 53.3 + - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 26.2 + - - +
30A GLY* 5.7 1.0 - - - -
31A GLN* 3.7 20.4 + - - -
67A SER 3.1 19.0 + - - -
68A ASP* 3.7 6.7 - - - -
70A VAL* 1.3 77.9 - - - +
72A SER* 1.3 57.4 + - - +
75A PHE* 2.9 36.5 + - - +
76A GLY 3.3 4.5 + - - +
77A ASN* 4.8 4.1 + - - -
----------------------------------------------------------
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 2.8 22.0 + - - -
69A LEU* 3.3 6.1 - - - -
71A SER* 1.3 77.6 - - - +
73A ALA* 1.3 60.2 - - - +
76A GLY* 2.7 31.0 + - - +
77A ASN* 2.9 29.6 + - - +
81A PHE* 3.7 17.6 - - - -
201A FOL 3.5 14.4 + - - -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 2.8 17.3 + - - +
70A VAL* 3.4 8.3 - - + +
72A SER* 1.3 78.7 - - - +
74A ILE* 1.3 63.7 + - + +
----------------------------------------------------------
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 5.0 2.9 - - + -
70A VAL* 2.9 37.7 + - + +
73A ALA* 1.3 82.9 - - + +
75A PHE* 1.3 95.0 + - + +
76A GLY 3.7 0.2 - - - -
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.6 26.5 - - + -
28A VAL* 5.7 5.6 - - + -
31A GLN* 3.5 49.8 - - + +
71A SER* 2.9 23.4 + - - +
74A ILE* 1.3 98.6 - - + +
76A GLY* 1.3 68.2 + - - +
77A ASN* 6.0 0.2 - - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 5.5 1.6 + - - +
33A LYS* 5.6 2.8 + - - -
71A SER 3.3 2.8 + - - -
72A SER* 2.7 28.0 + - - -
75A PHE* 1.3 81.8 - - - +
77A ASN* 1.3 70.1 + - - -
78A LEU 4.3 0.2 + - - -
----------------------------------------------------------
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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) + - + + + + + -
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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