Contacts of the helix formed by residues 33 - 68 (chain A) in PDB entry 2Y01
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 ALA 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 1.3 69.0 + - + +
35A LEU* 3.2 10.7 - - - +
36A LEU* 3.3 23.8 + - - +
37A SER* 3.2 20.3 + - - -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 1.3 81.5 - - + +
35A LEU* 1.3 59.3 + - + +
37A SER* 3.6 8.9 + - - -
38A GLN* 3.1 39.4 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 3.2 7.1 - - - +
34A GLU* 1.3 77.3 - - + +
36A LEU* 1.3 60.5 + - - +
37A SER 3.2 0.2 - - - -
38A GLN* 3.3 22.0 + - + +
39A GLN* 3.0 30.1 + - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.3 24.2 + - - +
35A LEU* 1.3 80.1 - - - +
37A SER* 1.3 59.9 + - - +
39A GLN* 3.6 19.9 + - - +
40A TRP* 3.1 25.2 + - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 3.2 9.9 + - - -
34A GLU* 3.6 12.2 + - - -
35A LEU 3.2 0.4 - - - -
36A LEU* 1.3 78.0 - - - +
38A GLN* 1.3 55.0 + - - +
40A TRP* 3.3 5.6 + - - +
41A GLU* 2.8 53.3 + - - +
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.1 29.7 + - - +
35A LEU* 3.3 23.8 + - + +
37A SER* 1.3 78.2 + - - +
39A GLN* 1.3 62.5 + - - +
41A GLU* 4.0 5.4 - - - +
42A ALA* 3.1 26.3 + - - +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 3.0 15.5 + - - +
36A LEU* 3.9 21.9 - - - +
38A GLN* 1.3 76.6 - - - +
40A TRP* 1.3 62.0 + - - +
42A ALA* 4.2 2.8 - - - +
43A GLY* 3.2 19.9 + - - -
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 3.1 15.9 + - - +
37A SER* 3.7 5.2 - - - +
39A GLN* 1.3 77.0 - - - +
41A GLU* 1.3 74.0 + - + +
42A ALA 3.3 0.2 + - - -
43A GLY 3.4 0.7 + - - -
44A MET* 2.9 63.6 + - + +
102A VAL* 3.3 42.2 - - + -
103A VAL* 3.7 16.8 - - - -
504A 2CV 6.0 3.1 - - + -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.8 36.5 + - - +
38A GLN* 4.0 6.1 - - - +
40A TRP* 1.3 80.3 - - + +
42A ALA* 1.3 54.3 + - - +
44A MET* 4.7 0.4 - - - -
45A SER* 2.7 37.7 + - - -
103A VAL* 3.6 34.3 - - + +
104A ARG* 4.0 27.7 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN 3.1 18.8 + - - +
39A GLN* 4.2 3.1 - - - +
41A GLU* 1.3 78.4 - - - +
43A GLY* 1.3 61.9 + - - +
45A SER* 3.6 6.8 + - - -
46A LEU* 3.2 26.2 + - - +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 3.2 15.8 + - - -
42A ALA* 1.3 75.1 - - - +
44A MET* 1.3 61.3 + - - +
46A LEU* 3.3 9.0 + - - +
47A LEU* 3.1 27.0 + - - +
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 2.9 64.3 + - + +
41A GLU 4.1 0.4 - - - +
43A GLY* 1.3 74.5 - - - +
45A SER* 1.3 61.0 + - - +
47A LEU* 3.3 24.2 + - + +
48A MET* 2.9 39.2 + - + +
102A VAL* 4.1 20.4 - - + -
103A VAL* 4.1 14.6 - - + -
504A 2CV 4.9 14.8 - - - -
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 2.7 23.9 + - - -
42A ALA* 3.6 7.9 - - - -
44A MET* 1.3 77.7 - - - +
46A LEU* 1.3 57.6 + - - +
48A MET* 3.9 4.5 - - - +
49A ALA* 3.1 27.7 + - - +
103A VAL* 3.5 23.1 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 3.2 13.4 + - - +
43A GLY* 3.4 13.2 - - - +
44A MET 3.2 0.4 - - - -
45A SER* 1.3 77.1 - - - +
47A LEU* 1.3 65.1 + - - +
49A ALA* 3.6 5.4 + - - +
50A LEU* 3.2 21.1 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.1 12.3 + - - +
44A MET* 3.3 30.7 + - + +
46A LEU* 1.3 75.5 - - - +
48A MET* 1.3 67.6 + - - +
50A LEU* 3.0 23.4 + - + +
51A VAL* 3.0 29.4 + - + +
504A 2CV 4.3 39.3 - - + +
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 2.9 30.5 + - + +
45A SER* 3.9 5.8 - - - +
47A LEU* 1.3 79.3 - - - +
49A ALA* 1.3 57.2 + - - +
51A VAL* 3.3 11.1 + - + +
52A VAL* 3.0 33.3 + - - +
95A VAL* 3.6 17.3 - - + -
99A ALA* 3.6 34.3 - - + -
102A VAL* 5.2 8.5 - - - -
103A VAL* 4.3 9.4 - - + -
330A TRP* 3.4 42.4 - - + -
504A 2CV 5.0 15.5 - - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER 3.1 19.0 + - - +
46A LEU* 3.8 7.2 - - - +
48A MET* 1.3 72.5 - - - +
50A LEU* 1.3 60.4 + - - +
52A VAL* 3.4 8.4 + - - +
53A LEU* 2.9 37.4 + - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU 3.2 11.8 + - - +
47A LEU* 3.0 26.1 + - + +
49A ALA* 1.3 79.3 - - - +
51A VAL* 1.3 59.5 + - + +
53A LEU* 3.2 13.0 + - + +
54A LEU* 2.8 49.4 + - + +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.0 22.9 + - + +
48A MET* 3.3 15.2 + - + +
50A LEU* 1.3 76.4 - - + +
52A VAL* 1.3 66.6 + - - +
54A LEU* 3.3 8.0 + - + +
55A ILE* 3.0 47.7 + - + +
95A VAL* 4.2 15.9 - - + -
330A TRP* 5.6 3.1 - - + -
333A TYR* 5.9 1.6 - - + +
334A ALA* 5.8 6.7 - - - -
504A 2CV 3.3 37.7 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 3.0 18.1 + - + +
49A ALA* 3.6 10.8 - - - +
51A VAL* 1.3 74.7 - - - +
53A LEU* 1.3 57.4 + - + +
55A ILE* 3.2 5.9 + - - -
56A VAL* 2.8 42.3 + - + +
91A GLY 3.6 22.4 - - - +
92A LEU* 5.7 1.1 - - + -
95A VAL* 3.8 20.4 - - + -
96A PRO* 4.3 15.9 - - + -
99A ALA* 5.9 0.9 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 2.9 22.9 + - + +
50A LEU* 3.2 13.4 + - + +
52A VAL* 1.3 78.6 - - + +
54A LEU* 1.3 58.6 + - - +
56A VAL* 4.9 2.7 - - - -
57A ALA* 2.8 41.5 + - + +
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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
----------------------------------------------------------
50A LEU* 2.8 33.0 + - + +
51A VAL* 3.7 9.0 - - + +
53A LEU* 1.3 77.2 - - - +
55A ILE* 1.3 56.2 + - - +
57A ALA* 4.9 2.0 - - + -
58A GLY* 3.1 27.8 + - - +
337A ALA* 4.4 25.9 - - + +
340A PRO* 5.6 0.3 - - - +
341A ILE* 5.0 17.5 - - + -
504A 2CV 5.7 6.1 - - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.0 40.5 + - + +
52A VAL 3.7 4.0 - - - +
54A LEU* 1.3 77.7 - - - +
56A VAL* 1.3 60.3 + - - +
59A ASN* 2.9 32.0 + - - +
87A ASP 3.4 25.8 - - - +
88A LEU* 4.7 1.1 - - - +
90A VAL* 4.5 0.2 - - + -
91A GLY* 3.4 18.4 - - - +
95A VAL* 4.2 16.4 - - + -
333A TYR 4.1 18.2 - - - +
334A ALA* 5.5 0.7 - - - -
336A SER* 3.8 18.2 - - - +
337A ALA* 3.7 24.9 - - + +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.8 31.4 + - + +
53A LEU* 4.2 2.7 - - - +
55A ILE* 1.3 71.1 - - - +
57A ALA* 1.3 66.2 + - - +
59A ASN 3.5 0.2 + - - -
60A VAL* 3.0 34.5 + - + +
88A LEU* 4.0 17.5 - - + +
91A GLY* 3.9 27.8 - - - +
92A LEU* 4.1 23.1 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 2.8 28.4 + - + +
54A LEU* 4.5 2.2 - - + +
56A VAL* 1.3 73.3 - - - +
58A GLY* 1.3 64.5 + - - +
60A VAL* 3.8 4.3 - - - +
61A LEU* 2.9 36.2 + - + +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.1 18.3 + - - +
57A ALA* 1.3 81.0 - - - +
59A ASN* 1.3 54.9 + - - +
61A LEU* 3.5 11.1 - - - +
62A VAL* 3.3 19.1 + - - +
340A PRO* 3.3 34.0 - - - +
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 2.9 27.2 + - - +
56A VAL 4.4 0.4 - - - +
57A ALA 3.2 0.4 - - - -
58A GLY* 1.3 72.8 - - - +
60A VAL* 1.3 64.5 + - - +
61A LEU 3.3 0.9 - - - -
62A VAL* 3.4 5.0 + - - +
63A ILE* 3.1 31.1 + - - +
84A ALA* 3.7 31.0 - - - +
87A ASP* 3.4 20.5 - - - +
88A LEU* 4.5 9.6 - - + -
336A SER 2.8 28.1 + - - -
339A ASN* 5.1 2.4 - - - +
340A PRO* 3.7 18.8 - - - +
343A TYR* 6.1 0.2 - - - -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.0 35.4 + - + +
57A ALA* 3.8 3.6 - - - +
59A ASN* 1.3 72.5 - - - +
61A LEU* 1.3 64.8 + - + +
63A ILE* 3.2 7.4 + - + +
64A ALA* 2.7 37.2 + - + +
88A LEU* 4.3 16.5 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 2.9 29.0 + - + +
58A GLY* 3.5 8.7 - - - +
59A ASN 3.3 0.2 - - - -
60A VAL* 1.3 80.3 - - + +
62A VAL* 1.3 56.3 + - - +
64A ALA* 3.9 2.9 - - + -
65A ALA* 2.8 34.1 + - - +
353A PHE* 3.7 24.5 - - + -
356A LEU* 3.9 32.8 - - + +
357A LEU* 4.1 37.5 - - + -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.3 15.3 + - - +
59A ASN* 3.7 10.1 - - - +
60A VAL 3.2 0.6 - - - -
61A LEU* 1.3 75.8 - - - +
63A ILE* 1.3 62.5 + - - +
65A ALA* 3.9 1.6 - - - +
66A ILE* 3.2 41.8 + - + +
80A ILE* 4.2 7.0 - - + -
81A THR* 5.6 0.2 - - - -
84A ALA* 4.2 15.3 - - + -
340A PRO* 3.9 16.2 - - + -
343A TYR* 3.7 38.1 - - + -
349A PHE* 4.6 3.1 - - + -
353A PHE* 4.0 14.6 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN 3.1 18.6 + - - +
60A VAL* 3.8 6.3 - - + +
62A VAL* 1.3 77.1 - - - +
64A ALA* 1.3 50.9 + - - +
66A ILE* 3.3 4.7 + - - +
67A GLY* 2.8 33.3 + - - -
81A THR* 4.4 23.1 - - + -
84A ALA* 3.8 23.6 - - + -
85A CYS* 4.2 17.3 - - - -
88A LEU* 3.9 26.5 - - + -
402A Y01 4.8 4.3 - - - +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 2.7 29.7 + - + +
61A LEU* 4.6 0.9 - - + -
63A ILE* 1.3 72.2 - - - +
65A ALA* 1.3 62.3 + - - +
67A GLY* 3.4 2.5 + - - +
68A SER* 2.8 30.8 + - - -
356A LEU* 3.9 25.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 2.8 22.2 + - - +
62A VAL 3.9 4.3 - - - +
64A ALA* 1.3 71.6 - - - +
66A ILE* 1.3 59.5 + - - +
68A SER* 4.2 1.8 - - - -
69A THR* 2.7 34.3 + - - -
72A LEU* 3.6 10.7 - - + +
349A PHE* 4.5 4.3 - - + -
352A ALA* 3.7 25.4 - - + -
353A PHE* 4.2 12.8 - - + -
356A LEU* 3.5 12.4 - - + +
----------------------------------------------------------
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.2 34.0 + - + +
63A ILE 3.8 2.9 - - - +
64A ALA 3.2 0.4 - - - -
65A ALA* 1.3 72.7 - - - +
67A GLY* 1.3 60.6 + - - +
68A SER 3.0 10.0 + - - -
69A THR 3.6 4.5 + - - +
72A LEU* 3.6 26.7 - - + +
73A GLN* 3.4 23.3 + - + +
77A ASN* 3.8 22.0 - - + +
78A LEU* 5.9 2.0 - - + -
80A ILE* 4.1 11.4 - - + -
81A THR* 3.6 27.1 - - - +
349A PHE* 3.9 21.1 - - + -
402A Y01 4.4 12.3 - - - +
----------------------------------------------------------
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 2.8 17.6 + - - -
64A ALA* 3.4 3.5 + - - -
66A ILE* 1.3 77.3 - - - +
68A SER* 1.3 58.2 + - - +
69A THR 3.8 0.2 - - - -
73A GLN* 3.8 9.7 + - - -
402A Y01 3.5 21.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 2.8 19.5 + - - -
65A ALA* 3.8 1.6 + - - -
66A ILE 3.0 0.8 - - - -
67A GLY* 1.3 80.0 - - - +
69A THR* 1.3 60.1 + - - +
70A GLN* 4.2 7.0 - - - +
73A GLN* 4.4 2.2 - - - +
355A ARG* 3.1 31.8 + - - -
356A LEU* 4.5 6.8 - - - +
----------------------------------------------------------
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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).
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