Contacts of the helix formed by residues 13 - 44 (chain B) in PDB entry 5AM8
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 ASP 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 2.5 35.9 + - - -
12B ALA* 1.3 78.1 + - - +
14B GLU* 1.3 66.1 + - - +
15B ALA* 3.5 9.3 + - - +
16B GLY 2.9 14.4 + - - -
17B ALA* 3.0 21.0 + - - +
76B TYR* 3.7 2.3 - - - -
79B ILE* 3.9 7.9 - - - -
83B PHE* 4.0 6.3 - - - -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 1.3 74.2 - - - +
15B ALA* 1.3 61.9 + - - +
17B ALA* 3.4 2.2 + - - +
18B GLN* 3.1 29.0 + - + +
83B PHE* 3.3 34.9 - - + -
84B THR* 2.9 48.5 + - - +
85B ASP* 3.3 22.2 + - - +
88B LEU* 4.0 9.3 - - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 4.5 2.0 - - - +
13B ASP* 3.2 12.0 + - - +
14B GLU* 1.3 80.0 - - - +
16B GLY* 1.3 63.1 + - - +
18B GLN* 3.5 12.9 + - - +
19B LEU* 3.5 17.9 + - - +
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 4.0 3.2 - - - -
11B SER* 3.2 32.5 + - - -
13B ASP* 2.9 11.7 + - - -
15B ALA* 1.3 74.9 - - - +
17B ALA* 1.3 52.8 + - - +
19B LEU* 3.0 14.0 + - - +
20B PHE* 2.8 32.9 + - - +
76B TYR* 3.2 7.0 - - - -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP 3.0 8.5 + - - +
14B GLU 3.6 8.1 - - - +
16B GLY* 1.3 74.7 - - - +
18B GLN* 1.3 57.2 + - - +
20B PHE* 3.4 5.1 - - - +
21B ALA* 2.8 31.2 + - - +
76B TYR* 3.0 18.1 + - + -
83B PHE* 3.5 32.8 - - + -
88B LEU* 3.6 7.7 - - + +
92B ILE* 3.8 14.6 - - + -
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.1 24.1 + - + +
15B ALA* 3.7 10.5 - - - +
16B GLY 3.2 0.2 - - - -
17B ALA* 1.3 75.2 - - - +
19B LEU* 1.3 59.7 + - + +
21B ALA* 3.3 5.2 + - - +
22B GLN* 3.0 44.1 + - - +
85B ASP* 2.9 36.9 + - - +
88B LEU* 3.7 20.4 - - + +
91B ILE* 6.2 0.2 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.6 15.6 - - + -
15B ALA 3.5 13.0 + - - +
16B GLY* 3.0 11.5 + - - +
18B GLN* 1.3 75.5 - - + +
20B PHE* 1.3 60.6 + - - +
22B GLN* 3.2 19.9 + - - +
23B SER* 2.9 30.8 + - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.5 33.5 - + + -
16B GLY 2.8 16.4 + - - +
17B ALA* 3.2 10.3 + - - +
19B LEU* 1.3 72.5 - - - +
21B ALA* 1.3 58.7 + - - +
23B SER* 3.3 1.7 + - - -
24B TYR* 2.7 39.6 + - + +
68B TRP* 3.6 35.6 - + - -
71B LYS* 3.7 22.9 - - + -
72B ALA* 3.6 33.4 - - + -
75B LEU* 4.4 1.6 - - + -
76B TYR* 3.8 26.0 - + - +
91B ILE* 6.1 0.9 - - + -
92B ILE* 4.8 12.3 - - + -
95B VAL* 4.3 13.0 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA 2.8 16.8 + - - +
18B GLN* 3.7 6.5 - - - +
20B PHE* 1.3 83.1 - - + +
22B GLN* 1.3 58.7 + - + +
24B TYR* 3.6 6.8 - - - +
25B GLN* 3.0 29.3 + - - +
88B LEU* 3.9 18.2 - - + -
91B ILE* 4.0 29.1 - - + +
92B ILE* 5.8 0.4 - - + -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN* 3.0 32.9 + - - +
19B LEU* 3.2 23.1 + - - +
21B ALA* 1.3 78.4 - - + +
23B SER* 1.3 61.3 + - - +
25B GLN* 3.5 7.7 + - - +
26B SER* 3.1 21.8 + - - -
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 5.4 1.0 + - - -
10B PHE* 3.6 24.7 - - - -
19B LEU 2.9 16.2 + - - -
20B PHE 3.7 1.1 - - - -
22B GLN* 1.3 75.1 - - - +
24B TYR* 1.3 68.4 + - - +
26B SER* 3.2 8.6 + - - -
27B SER* 3.2 23.2 + - - -
68B TRP* 3.6 13.9 - - - -
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Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 2.7 25.5 + - + +
21B ALA* 3.6 9.4 - - - +
23B SER* 1.3 73.3 - - - +
25B GLN* 1.3 55.9 + - + +
27B SER* 3.2 1.0 + - - -
28B ALA* 2.7 54.1 + - + +
32B LEU* 5.6 2.9 - - - +
64B PHE* 3.5 24.2 - + - -
65B ALA* 6.2 1.1 - - - -
68B TRP* 3.5 46.3 - + + -
91B ILE* 5.0 4.7 - - + -
95B VAL* 3.6 37.4 - - + +
377B VAL* 4.1 9.0 - - + +
378B SER* 3.9 15.7 + - - -
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 3.0 17.1 + - - +
22B GLN* 3.9 7.3 + - - +
24B TYR* 1.3 82.2 - - + +
26B SER* 1.3 65.8 + - - +
28B ALA* 4.1 4.7 - - - -
29B GLU* 3.1 37.3 + - + +
340B ARG* 5.7 2.0 - - - +
375B LEU 3.7 0.9 - - - +
376B PRO* 3.1 13.4 - - + +
377B VAL* 2.7 36.4 + - + +
380B ARG* 3.4 15.1 + - - +
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN 3.1 14.9 + - - -
23B SER* 3.2 11.6 + - - -
25B GLN* 1.3 80.9 - - - +
27B SER* 1.3 61.6 + - - +
29B GLU* 4.0 7.2 + - - +
30B GLN* 3.0 25.6 + - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY 3.7 18.4 + - - -
5B LEU* 3.8 17.6 + - - +
23B SER* 3.2 11.6 + - - -
24B TYR 3.9 3.6 - - - -
26B SER* 1.3 79.0 + - - +
28B ALA* 1.3 64.9 + - - +
30B GLN* 3.0 24.2 + - - +
31B VAL* 3.1 14.4 + - - +
64B PHE* 3.6 22.4 - - - -
68B TRP* 4.3 6.2 - - - -
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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
----------------------------------------------------------
24B TYR* 2.7 47.2 + - + +
25B GLN 4.0 2.9 - - - +
27B SER* 1.3 71.1 - - - +
29B GLU* 1.3 54.9 + - - +
31B VAL* 4.4 1.3 - - - +
32B LEU* 2.7 47.4 + - + +
64B PHE* 3.5 20.5 - - + -
377B VAL* 4.0 11.9 - - + -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 3.1 33.7 + - + +
26B SER* 4.3 6.0 - - - +
28B ALA* 1.3 76.4 - - - +
30B GLN* 1.3 58.8 + - + +
32B LEU* 4.7 3.4 - - - -
33B PHE* 3.0 29.1 + - - +
338B TYR* 3.2 23.4 - - - +
339B ASN* 4.7 5.3 - - - +
340B ARG* 2.7 35.8 + - - -
377B VAL* 4.3 10.1 - - + -
380B ARG* 2.6 33.7 + - - -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.0 20.7 - - + +
26B SER* 3.0 27.8 + - - +
27B SER* 3.0 15.1 + - - +
29B GLU* 1.3 75.5 - - + +
31B VAL* 1.3 62.0 + - + +
33B PHE* 3.7 7.2 - - - +
34B GLN* 3.1 29.1 + - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 5.2 1.6 - - + -
5B LEU* 4.1 23.3 - - + -
27B SER 3.1 15.0 + - - +
28B ALA* 3.9 2.5 - - - +
30B GLN* 1.3 75.3 - - - +
32B LEU* 1.3 67.8 + - + +
34B GLN* 3.1 36.0 + - - +
35B SER* 3.1 5.0 + - - -
60B LEU* 4.6 5.8 - - + +
61B SER* 3.5 33.4 - - - +
64B PHE* 3.7 39.9 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 5.6 3.1 - - - +
28B ALA* 2.7 34.0 + - + +
31B VAL* 1.3 73.2 - - + +
33B PHE* 1.3 58.6 + - - +
35B SER* 3.2 8.5 + - - -
36B VAL* 2.9 35.6 + - + +
61B SER* 5.8 2.5 - - - +
64B PHE* 6.3 1.1 - - + -
337B PHE 4.4 0.4 - - - -
338B TYR* 3.9 34.5 - - + -
377B VAL* 3.6 31.2 - - + -
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU 3.0 23.5 + - - +
30B GLN* 3.7 7.4 - - - +
32B LEU* 1.3 75.9 - - - +
34B GLN* 1.3 64.5 + - + +
36B VAL* 3.2 1.8 + - - +
37B ALA* 2.8 43.3 + - + +
337B PHE* 3.4 42.4 + + + +
339B ASN* 3.4 32.8 - - + -
342B ASP* 4.3 5.4 - - - -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN 3.1 18.2 + - - +
31B VAL* 3.1 29.3 + - - +
33B PHE* 1.3 83.7 - - + +
35B SER* 1.3 68.7 + - - +
37B ALA* 3.9 4.8 - - - +
38B ALA* 3.1 24.8 + - - +
57B ALA* 3.1 44.5 + - - +
60B LEU* 3.8 26.5 - - + +
61B SER* 3.5 8.7 + - - -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL 3.1 15.8 + - - -
32B LEU* 3.6 9.0 - - - -
33B PHE 3.1 0.4 - - - -
34B GLN* 1.3 82.3 - - - +
36B VAL* 1.3 65.8 + - - +
38B ALA* 3.3 2.9 + - - +
39B SER* 3.0 28.1 + - - -
54B GLN* 5.1 4.9 + - - +
57B ALA* 4.0 12.9 + - - +
58B ALA* 5.0 3.6 + - - -
61B SER* 3.6 18.6 + - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 2.9 22.3 + - + +
33B PHE 3.9 2.9 - - - +
35B SER* 1.3 76.9 - - - +
37B ALA* 1.3 57.8 + - - +
39B SER* 3.3 7.3 + - - -
40B TRP* 2.9 27.0 + - - +
335B TRP* 3.6 23.9 - - + -
336B ASP 3.6 21.5 - - - +
337B PHE* 3.6 30.3 - - + -
338B TYR* 4.0 16.4 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 2.8 37.8 + - + +
34B GLN* 3.9 7.6 - - - +
36B VAL* 1.3 72.7 - - - +
38B ALA* 1.3 57.8 + - - +
40B TRP* 3.3 4.3 + - - +
41B ALA* 3.0 27.9 + - - +
337B PHE* 3.8 17.6 - - + -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN 3.1 17.9 + - - +
35B SER 3.8 4.3 - - - +
37B ALA* 1.3 75.8 - - - +
39B SER* 1.3 64.2 + - - +
41B ALA* 3.3 7.5 + - - +
42B HIS* 3.0 23.4 + - - +
50B ASN 4.6 1.9 - - - +
53B ARG* 4.1 8.5 - - + +
54B GLN* 3.8 28.7 - - - +
57B ALA* 3.9 11.9 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.0 17.2 + - - -
36B VAL* 3.7 8.6 - - - -
38B ALA* 1.3 73.2 - - - +
40B TRP* 1.3 60.3 + - - +
42B HIS* 3.6 1.9 - - - +
43B ASP* 2.8 38.6 + - - +
54B GLN* 3.7 27.0 + - - +
335B TRP* 3.7 18.4 - - - -
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Residues in contact with TRP 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 2.9 15.1 + - - +
37B ALA 3.5 9.4 - - - +
38B ALA 3.2 0.2 - - - -
39B SER* 1.3 77.4 - - - +
41B ALA* 1.3 56.0 + - - +
43B ASP* 4.7 0.2 - - - -
44B THR* 2.7 64.6 + - + +
316B GLY 3.3 20.6 + - - -
318B MET* 3.9 9.9 - - + -
335B TRP* 3.5 40.1 - + + -
337B PHE* 4.0 14.8 - + + -
344B ARG* 3.1 45.9 - - + +
345B ILE 3.7 20.0 - - - -
346B LYS* 3.7 24.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA 3.0 17.0 + - - +
38B ALA* 3.6 9.0 - - - +
40B TRP* 1.3 80.2 - - - +
42B HIS* 1.3 61.0 + - - +
44B THR* 3.8 4.3 + - - -
45B ASN* 3.3 27.2 + - - +
50B ASN* 3.4 16.2 + - + +
53B ARG* 6.5 1.6 - - + -
----------------------------------------------------------
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 3.0 16.8 + - - +
39B SER* 3.6 5.4 - - - +
41B ALA* 1.3 75.7 - - - +
43B ASP* 1.3 84.9 + - - +
45B ASN 2.8 32.2 + - - -
46B ILE* 3.0 39.3 + - + +
47B THR 4.3 5.4 - - - -
50B ASN* 3.8 13.4 - - - +
51B ALA* 3.7 36.8 - - + +
54B GLN* 4.5 7.4 - - + +
116B SER* 4.8 10.2 + - - -
119B SER* 3.7 24.9 - - - -
120B ARG* 5.1 1.7 - - - +
329B VAL* 4.9 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 2.8 27.2 + - - +
40B TRP* 4.1 1.8 - - - +
42B HIS* 1.3 95.9 + - - +
44B THR* 1.3 58.3 + - - +
45B ASN 3.3 0.4 - - - -
119B SER* 4.5 2.1 + - - -
328B VAL* 3.5 3.9 - - - +
329B VAL* 2.9 50.8 + - + +
335B TRP* 3.3 24.1 - - + -
346B LYS* 3.9 20.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 2.7 61.5 + - + +
41B ALA* 3.8 5.4 + - - -
43B ASP* 1.3 78.0 - - - +
45B ASN* 1.3 56.4 + - - +
318B MET* 4.1 16.2 - - + -
326B ARG* 2.7 38.6 + - - -
328B VAL* 3.4 14.4 - - - +
346B LYS* 3.9 17.3 - - + -
----------------------------------------------------------
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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