Contacts of the helix formed by residues 26 - 59 (chain B) in PDB entry 5AJI
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 SER 26 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 1.3 82.1 + - - +
27B TYR* 1.3 59.8 + - - +
28B ALA* 3.3 3.4 - - - +
29B VAL* 3.1 32.2 - - - +
30B ASN* 3.7 7.3 - - - +
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 2.3 42.0 + - + +
26B SER* 1.3 67.8 - - - +
28B ALA* 1.3 67.0 + - - +
29B VAL 3.1 2.2 - - - -
30B ASN* 2.9 23.4 + - - +
31B ILE* 3.0 26.5 + - + +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.2 16.3 - - + +
26B SER* 5.1 1.1 - - - -
27B TYR* 1.3 79.2 - - - +
29B VAL* 1.3 55.7 + - - +
31B ILE* 3.3 12.1 + - - +
32B VAL* 2.9 37.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 3.1 37.8 + - - +
27B TYR 3.0 1.2 + - - -
28B ALA* 1.3 74.8 - - - +
30B ASN* 1.3 69.3 + - - +
32B VAL* 3.2 14.1 - - + +
33B ALA* 2.9 33.2 + - + +
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Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 3.7 13.7 - - - +
27B TYR* 2.9 14.4 + - - +
29B VAL* 1.3 79.1 - - - +
31B ILE* 1.3 58.0 + - + +
33B ALA* 3.6 6.1 - - - +
34B ALA* 2.7 35.5 + - - +
88B ARG* 3.1 40.7 + - - +
89B VAL* 4.2 7.1 - - + +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.0 27.9 + - + +
28B ALA* 3.3 11.4 + - - +
30B ASN* 1.3 77.6 - - + +
32B VAL* 1.3 64.1 + - + +
34B ALA* 3.5 7.0 + - - +
35B LEU* 3.2 33.2 + - + +
89B VAL* 4.3 20.4 - - + -
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 2.9 22.4 + - + +
29B VAL* 3.2 22.2 - - + +
31B ILE* 1.3 77.0 - - + +
33B ALA* 1.3 57.6 + - + +
35B LEU* 3.1 14.0 + - + +
36B ALA* 2.7 35.7 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 2.9 22.3 + - + +
30B ASN* 3.6 9.4 - - - +
32B VAL* 1.3 76.6 - - - +
34B ALA* 1.3 53.6 + - - +
36B ALA* 3.1 8.5 + - - +
37B ILE* 2.8 50.3 + - + +
88B ARG* 5.3 6.3 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN 2.7 22.3 + - - +
31B ILE 3.5 6.3 - - - +
32B VAL 3.3 0.2 - - - -
33B ALA* 1.3 73.4 - - - +
35B LEU* 1.3 63.7 + - + +
37B ILE* 4.3 6.0 - - - +
38B ILE* 3.1 31.5 + - + +
85B ALA* 3.4 20.2 - - + +
88B ARG* 5.1 1.3 - - + +
89B VAL* 3.3 27.4 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.2 23.8 + - + +
32B VAL* 3.1 16.0 + - + +
34B ALA* 1.3 76.2 - - + +
36B ALA* 1.3 61.0 + - - +
38B ILE* 3.1 18.1 + - + +
39B ILE* 2.8 44.2 + - + +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL 2.7 18.2 + - - +
33B ALA* 3.4 13.0 - - - +
35B LEU* 1.3 72.1 - - - +
37B ILE* 1.3 53.6 + - + +
39B ILE* 3.3 10.8 + - - +
40B VAL* 2.8 45.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 2.8 34.1 + - + +
34B ALA* 3.8 8.5 - - - +
36B ALA* 1.3 74.9 - - + +
38B ILE* 1.3 53.6 + - - +
40B VAL* 4.0 4.6 - - - +
41B GLY* 2.7 30.7 + - - -
81B THR* 3.2 32.9 - - + +
84B ALA* 4.3 16.2 - - + +
85B ALA* 3.9 14.1 - - + +
88B ARG* 4.4 17.9 - - + +
----------------------------------------------------------
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.1 25.8 + - + +
35B LEU* 3.5 21.1 - - + +
37B ILE* 1.3 75.1 - - - +
39B ILE* 1.3 60.7 + - + +
41B GLY 3.8 0.3 - - - -
42B LEU* 2.8 56.1 + - + +
81B THR* 3.6 10.3 - - + +
82B LEU* 5.1 17.9 - - + -
85B ALA* 3.6 17.5 - - + -
86B LEU* 6.2 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 2.8 35.4 + - + +
36B ALA* 3.7 7.9 - - - +
38B ILE* 1.3 80.0 - - + +
40B VAL* 1.3 65.3 - - + +
42B LEU* 3.2 9.0 + - + +
43B ILE* 3.0 46.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA* 2.8 29.5 + - + +
37B ILE* 4.0 5.2 - - - +
39B ILE* 1.3 74.6 - - + +
41B GLY* 1.3 57.7 + - - +
43B ILE* 3.5 9.6 + - + +
44B ILE* 2.9 38.5 + - + +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE 2.7 22.5 + - - -
40B VAL* 1.3 72.8 - - - +
42B LEU* 1.3 58.4 + - - +
44B ILE* 3.3 11.3 - - - +
45B ALA* 2.9 31.1 + - - +
77B ILE* 4.0 2.8 - - - +
78B ILE* 5.7 1.1 - - - -
81B THR* 3.5 23.8 - - - -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 2.8 46.3 + - + +
39B ILE* 3.7 8.1 - - + +
41B GLY* 1.3 76.1 - - - +
43B ILE* 1.3 58.8 + - + +
45B ALA* 3.4 4.7 + - - +
46B ARG* 3.1 31.7 + - - +
74B ARG* 5.5 7.7 + - - +
78B ILE* 3.7 31.9 - - + -
81B THR* 5.8 1.1 - - + -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.0 39.5 + - + +
40B VAL* 3.8 7.9 - - + +
42B LEU* 1.3 74.1 - - + +
44B ILE* 1.3 64.9 + - - +
45B ALA 3.1 2.3 + - - -
46B ARG* 3.3 9.3 + - + +
47B MET* 3.3 47.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 2.9 26.4 + - + +
41B GLY* 3.3 20.0 - - - +
43B ILE* 1.3 76.0 - - - +
45B ALA* 1.3 57.9 + - - +
47B MET* 4.1 8.7 - - + +
48B ILE* 3.3 44.6 + - + +
77B ILE* 4.3 11.9 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 2.9 19.1 + - - +
42B LEU 3.5 6.5 - - - +
43B ILE 3.1 0.2 - - - -
44B ILE* 1.3 75.6 - - - +
46B ARG* 1.3 58.8 + - - +
48B ILE* 3.4 0.9 + - - +
49B SER* 2.5 37.1 + - - -
74B ARG* 4.1 5.3 - - + +
77B ILE* 3.7 26.7 - - + +
78B ILE* 3.9 26.5 - - + -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 4.5 17.0 - - - +
42B LEU 3.1 14.6 + - - +
43B ILE* 3.5 12.3 - - + +
45B ALA* 1.3 78.0 - - - +
47B MET* 1.3 61.4 + - + +
49B SER* 3.0 15.8 + - - -
50B ASN* 3.0 32.8 + - - +
74B ARG* 3.9 33.0 - - - +
----------------------------------------------------------
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.3 38.6 + - + +
44B ILE* 4.4 7.9 - - + +
45B ALA 3.2 0.4 - - - -
46B ARG* 1.3 76.2 - - + +
48B ILE* 1.3 63.6 + - + +
50B ASN* 3.3 4.7 + - - +
51B ALA* 2.8 32.7 + - - +
54B ARG* 4.5 6.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.3 39.9 + - + +
47B MET* 1.3 78.8 - - + +
49B SER* 1.3 57.3 + - - +
51B ALA* 3.6 7.0 - - - +
52B VAL* 3.1 31.4 + - + +
73B VAL* 4.0 11.0 - - + -
77B ILE* 3.6 28.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 2.5 23.8 + - - -
46B ARG* 3.0 12.1 + - - -
48B ILE* 1.3 74.7 - - - +
50B ASN* 1.3 63.0 + - - +
52B VAL* 3.1 21.5 - - - +
53B ASN* 3.4 12.1 + - - +
67B R1A 5.0 5.8 - - - +
70B SER* 3.6 26.6 - - - -
73B VAL* 4.2 3.1 - - - -
74B ARG* 3.4 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.0 32.5 + - - +
47B MET* 3.9 3.0 - - - +
49B SER* 1.3 77.4 - - - +
51B ALA* 1.3 65.4 + - - +
52B VAL 3.3 0.2 - - - -
53B ASN* 2.9 7.7 + - - +
54B ARG* 2.9 54.7 + - + +
67B R1A 4.1 24.4 - - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET 2.8 17.9 + - - +
48B ILE* 3.6 8.3 - - - +
50B ASN* 1.3 76.3 - - - +
52B VAL* 1.3 61.8 + - - +
54B ARG* 3.5 23.1 + - - +
55B LEU* 3.1 24.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.1 19.8 + - + +
49B SER* 3.1 25.6 - - - +
51B ALA* 1.3 78.2 - - + +
53B ASN* 1.3 61.8 + - - +
55B LEU* 3.4 13.8 + - + +
56B MET* 3.1 36.1 + - + +
70B SER* 4.0 8.3 - - - +
73B VAL* 4.1 29.4 - - + -
----------------------------------------------------------
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER 3.4 11.7 - - - +
50B ASN* 2.9 11.8 + - - +
52B VAL* 1.3 78.1 - - - +
54B ARG* 1.3 65.5 + - + +
56B MET* 3.4 4.0 + - - +
57B ILE* 3.0 42.4 + - - +
66B ALA* 3.7 13.8 - - - +
67B R1A 3.8 40.0 + - - +
70B SER* 3.2 20.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET* 4.5 6.3 + - - +
50B ASN* 2.9 37.5 + - + +
51B ALA* 3.5 31.5 - - - +
53B ASN* 1.3 76.3 - - + +
55B LEU* 1.3 57.6 + - - +
57B ILE* 4.0 7.5 - - - +
58B SER* 2.8 35.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA 3.1 18.8 + - - +
52B VAL* 3.5 15.5 - - + +
53B ASN 3.2 0.2 - - - -
54B ARG* 1.3 78.0 - - - +
56B MET* 1.3 58.9 + - + +
58B SER* 2.9 20.6 + - - +
59B ARG* 3.1 31.4 + - + +
----------------------------------------------------------
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Residues in contact with MET 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.1 28.3 + - + +
53B ASN* 3.8 1.1 - - - +
55B LEU* 1.3 78.2 - - + +
57B ILE* 1.3 66.0 + - - +
59B ARG* 3.0 11.5 + - - -
60B LYS 3.3 0.2 + - - -
61B ILE* 3.1 49.1 + - + +
66B ALA* 3.4 31.4 - - + +
69B LEU* 4.0 30.5 - - + -
70B SER* 3.2 29.2 - - - +
73B VAL* 5.9 1.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN* 3.0 40.1 + - - +
54B ARG* 4.0 6.3 - - - +
56B MET* 1.3 75.7 - - - +
58B SER* 1.3 60.5 + - - +
60B LYS* 3.1 19.4 + - - +
61B ILE 4.0 11.6 + - - +
63B ALA* 4.6 18.2 - - + +
66B ALA* 4.0 11.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 2.8 16.8 + - - -
55B LEU* 2.9 24.9 + - - +
57B ILE* 1.3 78.0 - - - +
59B ARG* 1.3 58.3 + - - +
60B LYS* 3.2 14.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.1 27.6 + - + +
56B MET* 3.0 8.9 + - - +
58B SER* 1.3 78.2 + - - +
60B LYS* 1.3 70.4 + - - +
61B ILE* 3.2 17.1 + - + +
46C ARG* 4.9 16.2 - - - +
74C ARG* 6.1 0.6 - - - +
----------------------------------------------------------
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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