Contacts of the helix formed by residues 21 - 53 (chain A) in PDB entry 5CXV
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 GLY 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 1.3 73.0 - - - +
22A PRO* 1.3 70.5 - - - +
23A TRP 3.5 2.0 - - - -
24A GLN* 3.4 19.0 + - - -
25A VAL* 2.9 30.9 + - - +
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Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS 4.6 0.4 - - - +
21A GLY* 1.3 82.7 - - - +
23A TRP* 1.3 68.5 + - + +
25A VAL* 3.2 8.6 + - + +
26A ALA* 2.9 28.8 + - - +
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 3.5 0.2 - - - -
22A PRO* 1.3 86.7 - - + +
24A GLN* 1.3 64.2 + - - +
26A ALA* 3.2 9.2 + - + +
27A PHE* 2.9 25.7 + - - +
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.0 29.4 - - + +
21A GLY* 3.4 27.2 + - - +
22A PRO 3.3 0.4 - - - -
23A TRP* 1.3 78.6 - - - +
25A VAL* 1.3 62.3 + - - +
27A PHE* 3.3 4.3 + - - +
28A ILE* 2.9 47.7 + - + +
87A LEU* 4.7 0.2 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.0 20.2 - - + +
21A GLY 2.9 22.5 + - - +
22A PRO* 3.5 7.4 - - + +
24A GLN* 1.3 75.6 - - - +
26A ALA* 1.3 61.5 + - - +
29A GLY* 2.9 28.6 + - - -
87A LEU* 3.7 36.4 - - + +
88A MET* 4.4 19.5 - - + -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 2.9 16.9 + - - +
23A TRP* 3.6 10.1 - - + +
25A VAL* 1.3 79.1 - - - +
27A PHE* 1.3 64.0 + - - +
29A GLY* 5.2 0.2 - - - -
30A ILE* 2.9 39.2 + - + +
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP 2.9 17.6 + - - +
24A GLN* 3.8 4.5 - - - +
26A ALA* 1.3 77.4 - - - +
28A ILE* 1.3 76.5 + - + +
30A ILE* 3.7 3.2 - - - +
31A THR* 2.9 51.9 + - + +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.7 7.6 - - - -
24A GLN* 2.9 42.1 + - + +
27A PHE* 1.3 84.1 - - + +
29A GLY* 1.3 64.7 + - - +
31A THR* 3.6 5.8 - - - -
32A THR* 3.0 45.6 + - + +
83A THR* 4.0 13.9 - - + -
86A LEU* 5.0 7.6 - - + -
87A LEU* 3.8 20.4 - - + -
405A TRP* 5.6 2.0 - - + +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL 2.9 19.0 + - - -
26A ALA 3.9 0.2 - - - -
28A ILE* 1.3 77.6 - - - +
30A ILE* 1.3 56.4 + - - +
32A THR* 3.8 4.7 + - - -
33A GLY* 2.9 26.0 + - - -
83A THR* 4.8 0.9 - - - -
87A LEU* 3.8 14.0 - - - +
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 2.9 30.2 + - + +
27A PHE* 3.8 4.7 - - - +
29A GLY* 1.3 76.2 - - - +
31A THR* 1.3 65.8 + - + +
33A GLY* 3.2 1.4 + - - -
34A LEU* 2.9 40.5 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 2.9 51.6 + - + +
28A ILE* 3.1 10.0 + - - -
30A ILE* 1.3 81.9 - - + +
32A THR* 1.3 66.5 + - - +
34A LEU* 3.2 12.7 + - + +
35A LEU* 2.9 27.1 + - - +
405A TRP* 5.6 2.9 - - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.0 34.5 + - + +
29A GLY* 3.8 2.8 + - - -
31A THR* 1.3 76.0 - - - +
33A GLY* 1.3 61.0 + - - +
35A LEU* 3.8 11.3 - - - +
36A SER* 2.9 27.4 + - - -
79A MET* 4.9 6.1 + - - +
80A ASN* 4.6 5.6 + - - -
83A THR* 3.2 25.0 + - + +
405A TRP* 3.2 42.6 - - + +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 2.9 20.5 + - - -
30A ILE* 3.5 1.6 - - - -
31A THR 3.1 0.2 - - - -
32A THR* 1.3 74.4 + - - +
34A LEU* 1.3 56.3 + - - +
36A SER* 2.7 26.7 + - - -
37A LEU* 2.9 25.8 + - - +
80A ASN* 4.6 8.1 - - - -
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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 ILE* 2.9 28.9 + - + +
31A THR* 3.2 12.8 + - + +
33A GLY* 1.3 70.7 - - - +
35A LEU* 1.3 63.7 + - - +
37A LEU* 3.4 10.5 + - + +
38A ALA* 2.9 25.4 + - - +
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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
----------------------------------------------------------
31A THR 2.9 16.1 + - - +
32A THR* 3.9 7.6 - - - +
34A LEU* 1.3 76.2 - - - +
36A SER* 1.3 57.0 - - - +
38A ALA* 3.4 6.3 + - - +
39A THR* 2.9 33.3 + - - -
79A MET* 3.4 35.2 - - + -
405A TRP* 4.4 25.6 - - + +
408A TYR* 5.0 0.7 - - + -
409A VAL* 4.2 29.8 - - + -
412A THR* 3.4 23.2 + - + +
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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 THR 2.9 15.0 + - - -
33A GLY* 2.7 16.4 + - - -
35A LEU* 1.3 71.6 - - - +
37A LEU* 1.3 60.8 + - - +
39A THR* 3.1 4.3 + - - -
40A VAL* 2.9 34.1 + - - +
75A GLY 2.8 14.4 + - - +
76A THR* 4.8 0.2 - - - -
79A MET* 3.5 14.8 - - - +
80A ASN* 2.6 36.5 + - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 2.9 36.0 + - - +
34A LEU* 4.2 10.3 - - + +
36A SER* 1.3 77.8 - - - +
38A ALA* 1.3 55.4 + - - +
40A VAL* 4.1 8.9 - - + +
41A THR* 2.6 39.3 + - - +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 2.9 17.9 + - - +
35A LEU* 3.7 7.0 - - - +
36A SER 3.2 0.2 - - - -
37A LEU* 1.3 75.7 - - - +
39A THR* 1.3 59.5 + - - +
41A THR* 3.9 3.9 - - - -
42A GLY* 2.9 26.5 + - - -
412A THR* 4.0 16.7 - - + +
415A PRO* 5.7 0.7 - - - +
416A MET* 5.4 9.3 - - + +
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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 LEU 2.9 10.5 + - - -
36A SER 3.1 6.9 + - - -
38A ALA* 1.3 74.0 - - - +
40A VAL* 1.3 65.6 + - - +
42A GLY* 5.3 0.2 - - - -
43A ASN* 2.9 42.5 + - - +
71A ASP 3.3 26.5 - - - +
72A LEU* 5.0 0.2 - - - -
75A GLY* 3.7 11.0 - - - -
79A MET* 3.4 10.7 - - + +
411A SER* 3.8 15.7 - - - +
412A THR* 2.5 34.8 + - - +
415A PRO* 5.8 0.4 - - - -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 2.9 23.2 + - - +
37A LEU* 4.1 7.4 - - + +
39A THR* 1.3 74.3 - - - +
41A THR* 1.3 61.0 + - - +
44A LEU* 2.8 47.8 + - + +
72A LEU* 3.8 16.9 - - + +
75A GLY* 3.8 25.6 - - - +
76A THR* 3.8 16.8 - - - +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.6 27.3 + - - +
38A ALA* 3.9 4.7 - - - -
40A VAL* 1.3 78.3 - - - +
42A GLY* 1.3 58.1 + - - +
44A LEU* 3.9 4.1 - - - +
45A LEU* 2.9 51.5 + - + +
433A LEU* 4.9 10.5 - - + -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 17.3 + - - -
39A THR 3.9 0.2 - - - -
41A THR* 1.3 77.6 - - - +
43A ASN* 1.3 62.9 + - - +
45A LEU* 3.0 12.6 + - - +
46A VAL* 3.0 22.5 + - - +
415A PRO* 4.1 17.7 - - - -
429A PHE* 4.1 5.1 - - - -
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Residues in contact with ASN 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 37.0 + - - +
42A GLY* 1.3 75.4 - - - +
44A LEU* 1.3 63.8 + - - +
46A VAL* 3.0 10.5 + - - +
47A LEU* 3.0 26.5 + - - +
68A ALA* 3.4 35.9 - - + +
71A ASP* 3.5 19.3 - - - +
72A LEU* 4.1 9.9 - - + -
411A SER 3.4 21.8 + - - -
415A PRO* 3.7 19.0 - - - +
418A TYR* 4.6 1.4 + - - -
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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 VAL* 2.8 35.7 + - + +
41A THR* 3.9 4.0 - - - +
43A ASN* 1.3 76.1 - - - +
45A LEU* 1.3 57.7 + - + +
47A LEU* 3.2 14.6 + - + +
48A ILE* 2.9 56.2 + - + +
72A LEU* 3.9 21.8 - - + +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.9 42.6 + - + +
42A GLY* 3.2 7.0 - - - +
44A LEU* 1.3 73.5 - - - +
46A VAL* 1.3 60.8 + - - +
48A ILE* 4.6 7.0 - - + +
49A SER* 2.9 32.9 + - - -
429A PHE* 3.3 38.4 - - + -
432A LEU* 4.2 31.6 - - + +
433A LEU* 4.1 30.3 - - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 3.0 14.1 + - - +
43A ASN* 3.0 9.4 + - - +
45A LEU* 1.3 76.6 - - - +
47A LEU* 1.3 64.1 + - - +
49A SER* 3.1 3.8 + - - -
50A PHE* 3.0 24.6 + - + +
64A LEU* 4.4 5.6 - - + +
65A LEU* 4.3 11.4 - - + +
68A ALA* 4.0 17.9 - - + -
415A PRO* 4.1 10.1 - - + -
418A TYR* 3.9 32.3 - - + +
419A ALA* 4.8 0.2 - - + -
425A PHE* 4.1 17.0 - - + -
429A PHE* 3.6 18.8 - - + -
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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 ASN 3.0 18.5 + - - +
44A LEU* 3.6 17.9 - - + +
46A VAL* 1.3 77.6 - - - +
48A ILE* 1.3 58.7 + - + +
50A PHE* 3.4 3.1 + - - +
51A LYS* 2.9 28.6 + - - +
65A LEU* 3.8 21.6 - - + +
68A ALA* 3.9 25.6 - - + +
69A CYS* 4.0 25.4 - - - -
72A LEU* 4.4 19.5 - - + -
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.9 47.0 + - + +
45A LEU* 4.3 6.3 - - + +
47A LEU* 1.3 72.7 - - + +
49A SER* 1.3 65.2 + - - +
51A LYS* 3.1 9.0 + - + +
52A VAL* 2.9 27.1 + - + +
432A LEU* 3.7 31.2 - - + -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 2.9 17.1 + - - -
46A VAL 3.1 8.5 + - - -
48A ILE* 1.3 76.5 - - - +
50A PHE* 1.3 66.0 + - - +
53A ASN* 2.9 30.5 + - - +
56A LEU* 3.4 15.2 - - - +
425A PHE* 3.4 12.0 - - - -
428A THR* 3.7 30.3 - - - -
429A PHE* 3.9 13.0 - - - -
432A LEU* 3.7 5.4 - - - +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.0 15.4 + - + +
47A LEU 3.6 4.0 - - - +
49A SER* 1.3 82.8 + - - +
51A LYS* 1.3 67.7 + - - +
52A VAL 3.4 0.2 + - - -
53A ASN 3.5 5.9 - - - +
56A LEU* 3.2 36.8 - - + -
57A LYS* 3.3 32.3 - - + +
61A ASN* 3.7 29.2 - - + -
62A TYR* 3.6 31.2 - + - -
65A LEU* 3.5 30.5 - - + -
425A PHE* 5.4 4.0 - + + -
502A Y01 3.6 29.6 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 2.9 17.4 + - - +
48A ILE* 3.1 9.8 + - + +
50A PHE* 1.3 82.2 - - - +
52A VAL* 1.3 59.6 + - + +
57A LYS* 3.4 21.0 + - - +
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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 ILE* 2.9 21.6 + - + +
49A SER* 3.9 4.0 - - - +
51A LYS* 1.3 78.6 - - + +
53A ASN* 1.3 59.5 + - - +
54A THR* 4.1 3.4 + - - +
57A LYS* 5.3 0.4 - - - -
428A THR* 4.1 14.8 - - + -
432A LEU* 4.4 11.4 - - + -
437A TRP* 3.3 52.0 + - + +
439A LYS* 5.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 2.9 14.7 + - - +
50A PHE 3.5 13.6 - - - +
52A VAL* 1.3 77.9 - - - +
54A THR* 1.3 64.9 + - - +
55A GLU* 3.0 34.0 + - - +
56A LEU* 3.2 22.4 + - + +
57A LYS* 3.5 3.1 - - - +
424A ALA* 4.3 3.6 + - - +
428A THR* 2.9 29.5 + - + +
437A TRP* 3.7 25.8 - - + -
----------------------------------------------------------
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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