Contacts of the helix formed by residues 13 - 44 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 2.6 35.2 + - - -
12A ALA* 1.3 78.2 - - - +
14A GLU* 1.3 66.8 + - - +
15A ALA* 3.9 9.4 - - - +
16A GLY 3.0 15.1 + - - -
17A ALA 3.0 17.7 + - - -
76A TYR* 3.6 5.4 - - - -
79A ILE* 4.5 3.8 - - - -
83A PHE* 4.4 6.1 - - - -
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 1.3 74.9 - - - +
15A ALA* 1.3 61.5 + - - +
17A ALA* 3.4 2.4 + - - +
18A GLN* 3.2 27.1 + - + +
83A PHE* 3.3 35.0 - - + -
84A THR* 2.8 50.8 + - - +
85A ASP* 3.4 17.2 + - - +
88A LEU* 3.6 14.9 - - + +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 5.1 0.4 - - - +
13A ASP* 3.2 10.0 + - - +
14A GLU* 1.3 78.7 - - - +
16A GLY* 1.3 62.0 + - - +
18A GLN* 3.2 23.6 + - - +
19A LEU* 3.4 12.2 + - - +
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Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.9 3.8 - - - +
11A SER* 3.2 30.9 + - - -
13A ASP* 3.0 11.3 + - - -
15A ALA* 1.3 72.6 - - - +
17A ALA* 1.3 58.7 + - - +
19A LEU* 3.1 13.8 + - - +
20A PHE* 2.8 25.5 + - - +
76A TYR* 3.1 10.0 + - - -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 3.0 10.3 + - - +
14A GLU 3.5 8.7 - - - +
15A ALA 3.3 0.2 - - - -
16A GLY* 1.3 76.6 - - - +
18A GLN* 1.3 55.0 + - - +
20A PHE* 3.4 3.3 - - - +
21A ALA* 2.9 30.7 + - - +
76A TYR* 3.1 26.3 + - + -
83A PHE* 3.6 29.6 - - + -
88A LEU* 3.5 10.2 - - + +
92A ILE* 4.3 4.9 - - + +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.2 20.9 + - + +
15A ALA* 3.2 11.2 + - - +
17A ALA* 1.3 75.7 - - - +
19A LEU* 1.3 60.4 + - + +
21A ALA* 3.5 4.3 + - - +
22A GLN* 3.0 44.0 + - - +
85A ASP* 2.9 31.1 + - - +
88A LEU* 3.5 29.2 - - - +
91A ILE* 6.0 0.5 - - - +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.5 17.1 - - + -
15A ALA 3.4 11.4 + - - +
16A GLY* 3.1 12.2 + - - +
18A GLN* 1.3 76.7 - - + +
20A PHE* 1.3 61.3 + - - +
22A GLN* 3.3 24.2 + - - +
23A SER* 2.9 30.1 + - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.5 33.1 - + + -
16A GLY 2.8 13.6 + - - +
17A ALA* 3.4 7.6 - - - +
19A LEU* 1.3 76.3 - - - +
21A ALA* 1.3 60.4 + - - +
23A SER* 3.2 3.3 + - - -
24A TYR* 2.8 30.8 + - + +
68A TRP* 3.6 46.4 - + - -
71A LYS* 3.6 25.8 - - + -
72A ALA* 3.8 17.5 - - + -
75A LEU* 4.1 2.2 - - + -
76A TYR* 3.7 19.7 - + - +
92A ILE* 3.8 25.4 - - + -
95A VAL* 4.2 12.6 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.9 17.2 + - - +
18A GLN* 3.7 6.3 - - - +
20A PHE* 1.3 81.6 - - - +
22A GLN* 1.3 63.0 + - + +
24A TYR* 3.5 7.5 + - - +
25A GLN* 3.1 23.2 + - - +
88A LEU* 3.9 17.5 - - + -
91A ILE* 3.9 29.9 - - + +
92A ILE* 4.7 2.5 - - + -
376A PRO* 6.0 0.7 - - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.0 35.2 + - - +
19A LEU* 3.6 25.3 - - - +
21A ALA* 1.3 75.9 - - - +
23A SER* 1.3 62.9 + - - +
25A GLN* 3.3 8.0 + - - +
26A SER* 3.0 22.7 + - - -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 5.4 0.9 + - - -
10A PHE* 3.5 24.5 - - - -
19A LEU 2.9 16.8 + - - -
20A PHE 3.2 1.5 + - - -
22A GLN* 1.3 73.7 - - - +
24A TYR* 1.3 66.8 + - - +
26A SER* 3.1 21.2 + - - -
27A SER* 3.4 7.6 + - - -
68A TRP* 3.5 17.2 - - - -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 2.8 19.2 + - + +
21A ALA* 3.5 13.0 - - - +
23A SER* 1.3 71.2 - - - +
25A GLN* 1.3 56.0 + - + +
27A SER* 3.1 5.4 + - - -
28A ALA* 2.8 51.6 + - + +
32A LEU* 5.4 5.9 - - - +
64A PHE* 3.5 24.7 - + - -
65A ALA* 6.0 2.2 - - - -
68A TRP* 3.4 46.9 - + + -
91A ILE* 5.0 4.7 - - + -
95A VAL* 3.9 26.2 - - + +
377A VAL* 4.0 9.4 - - + +
378A SER* 3.6 23.9 + - - -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 3.1 11.3 + - - +
22A GLN* 3.3 12.1 + - - +
24A TYR* 1.3 83.9 - - + +
26A SER* 1.3 64.2 + - - +
27A SER 3.2 0.9 + - - -
28A ALA* 3.4 9.6 + - - -
29A GLU* 3.2 44.2 + - - +
340A ARG* 3.2 17.1 - - - +
376A PRO* 3.4 16.4 - - + +
377A VAL* 2.8 35.1 + - - +
380A ARG* 3.3 8.1 - - - +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.0 13.8 + - - -
23A SER* 3.1 16.3 + - - -
25A GLN* 1.3 77.1 - - - +
27A SER* 1.3 58.3 + - - +
29A GLU* 5.7 2.1 - - - +
30A GLN* 4.0 12.5 + - - -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLY 3.3 23.4 + - - -
5A LEU* 3.7 16.0 - - - +
23A SER 3.4 7.1 + - - -
24A TYR 3.1 5.1 + - - -
26A SER* 1.3 80.6 + - - +
28A ALA* 1.3 64.2 + - - +
29A GLU 3.4 2.8 + - - -
30A GLN* 3.5 19.6 + - - +
31A VAL* 3.7 14.6 + - - +
64A PHE* 3.9 20.0 - - - -
68A TRP* 4.8 5.0 - - - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.8 47.3 + - + +
25A GLN 3.4 2.8 + - - +
27A SER* 1.3 74.7 - - - +
29A GLU* 1.3 66.9 + - - +
31A VAL* 3.2 1.9 + - - +
32A LEU* 3.0 33.1 + - + +
64A PHE* 3.7 15.0 - - + -
377A VAL* 3.9 15.7 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.6 24.3 + - - +
26A SER 5.7 2.0 - - - +
27A SER 3.4 1.0 - - - -
28A ALA* 1.3 78.0 - - - +
30A GLN* 1.3 57.7 + - + +
32A LEU* 4.1 3.0 - - - +
33A PHE* 2.9 32.3 + - - +
338A TYR 3.4 24.3 - - - +
339A ASN* 4.2 10.9 - - - +
340A ARG* 2.8 24.6 + - - +
377A VAL* 3.7 9.6 - - + -
380A ARG* 2.7 29.8 + - - -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.3 15.1 - - + +
26A SER 4.0 18.8 + - - -
27A SER* 3.5 14.0 + - - +
28A ALA 3.3 0.8 - - - -
29A GLU* 1.3 78.7 - - + +
31A VAL* 1.3 61.6 + - + +
33A PHE* 3.7 7.4 - - - +
34A GLN* 3.1 29.2 + - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.2 22.0 - - + -
27A SER 3.7 13.9 + - - +
28A ALA 3.2 6.1 + - - +
30A GLN* 1.3 76.3 - - + +
32A LEU* 1.3 67.6 + - + +
34A GLN* 2.9 36.7 + - - +
35A SER 3.2 2.1 + - - -
60A LEU* 4.3 7.6 - - + +
61A SER* 3.7 34.3 + - - +
64A PHE* 4.0 39.3 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 5.4 6.3 - - - +
28A ALA* 3.0 24.3 + - + +
29A GLU 4.1 0.2 - - - +
31A VAL* 1.3 77.6 - - + +
33A PHE* 1.3 66.0 + - - +
35A SER* 3.2 7.5 + - - -
36A VAL* 2.9 27.9 + - + +
61A SER* 5.1 7.9 - - - +
64A PHE* 6.1 3.8 - - + -
337A PHE 4.5 0.2 - - - -
338A TYR* 3.9 44.9 - - + -
377A VAL* 4.1 24.2 - - + -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 2.9 21.4 + - - +
30A GLN* 3.7 7.9 - - - +
31A VAL 3.3 0.2 - - - -
32A LEU* 1.3 76.5 - - - +
34A GLN* 1.3 63.8 + - + +
36A VAL* 3.3 1.1 + - - +
37A ALA* 2.8 42.5 + - + +
337A PHE* 3.4 39.8 + + + +
339A ASN* 3.4 37.5 - - + -
342A ASP* 4.2 6.3 - - - -
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN 3.1 17.5 + - - +
31A VAL* 2.9 31.3 + - - +
33A PHE* 1.3 82.4 - - + +
35A SER* 1.3 68.8 + - - +
37A ALA* 4.0 4.1 - - - +
38A ALA* 3.1 24.8 + - - +
57A ALA* 3.1 44.6 + - - +
60A LEU* 3.7 27.9 - - + +
61A SER* 3.3 9.3 + - - -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 3.2 1.5 + - - -
32A LEU* 3.2 11.1 + - - -
34A GLN* 1.3 86.4 - - - +
36A VAL* 1.3 63.2 + - - +
38A ALA* 3.2 4.2 + - - +
39A SER* 2.9 29.1 + - - -
54A GLN* 5.0 4.5 + - - +
57A ALA* 3.9 10.4 - - - +
58A ALA* 4.7 9.0 + - - +
61A SER* 3.4 26.6 + - - -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.9 24.3 + - - +
33A PHE 3.9 2.7 - - - +
35A SER* 1.3 71.4 - - - +
37A ALA* 1.3 58.0 + - - +
39A SER* 3.2 7.0 + - - -
40A TRP* 2.8 27.9 + - - +
335A TRP* 3.7 23.3 - - + -
336A ASP 3.6 25.6 - - - +
337A PHE* 3.6 27.4 - - + -
338A TYR* 3.8 19.3 - - + -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 2.8 42.2 + - + +
34A GLN* 4.0 5.2 - - - +
36A VAL* 1.3 73.2 - - - +
38A ALA* 1.3 57.4 + - - +
40A TRP* 3.3 3.7 + - - +
41A ALA* 3.0 28.8 + - - +
337A PHE* 3.8 14.7 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN 3.1 19.0 + - - +
35A SER 3.6 4.0 - - - +
37A ALA* 1.3 73.4 - - - +
39A SER* 1.3 65.5 + - - +
41A ALA* 3.4 7.7 + - - +
42A HIS* 3.1 22.7 + - - +
50A ASN 4.6 1.9 - - - +
53A ARG* 4.1 8.0 - - + +
54A GLN* 3.8 19.4 - - + +
57A ALA* 3.6 22.0 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 2.9 20.9 + - - -
36A VAL* 3.6 6.5 - - - -
38A ALA* 1.3 74.7 - - - +
40A TRP* 1.3 59.8 + - - +
42A HIS* 3.3 1.5 + - - +
43A ASP* 2.9 36.9 + - - +
54A GLN* 3.5 28.7 + - - -
335A TRP* 3.7 17.0 - - - -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL 2.8 14.0 + - - +
37A ALA 3.5 9.2 - - - +
39A SER* 1.3 75.6 - - - +
41A ALA* 1.3 64.8 + - - +
44A THR* 2.8 58.7 + - + +
316A GLY 3.3 20.2 + - - -
318A MET* 3.9 9.6 - - + -
335A TRP* 3.4 40.9 - + + -
337A PHE* 3.9 14.1 - + + -
344A ARG* 3.2 47.3 - - + +
345A ILE 3.7 20.6 - - - -
346A LYS* 3.8 24.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 3.0 16.7 + - - +
38A ALA* 3.6 8.3 - - - +
39A SER 3.3 0.2 - - - -
40A TRP* 1.3 80.9 - - + +
42A HIS* 1.3 62.1 + - - +
44A THR* 3.7 5.5 + - - -
45A ASN* 3.3 25.5 + - - +
50A ASN* 3.4 16.9 + - + +
53A ARG* 6.4 1.3 - - - -
----------------------------------------------------------
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 3.1 14.7 + - - +
39A SER* 3.7 7.9 - - - +
41A ALA* 1.3 76.2 - - - +
43A ASP* 1.3 81.0 + - - +
45A ASN 2.9 26.2 + - - -
46A ILE* 3.1 33.9 + - + +
47A THR 4.2 5.2 - - - -
50A ASN* 3.8 19.4 - - + +
51A ALA* 3.6 37.8 - - + +
54A GLN* 4.5 8.3 - - + +
116A SER* 4.7 12.3 + - - -
119A SER* 4.0 22.9 - - - -
120A ARG* 5.1 1.5 - - - +
329A VAL* 5.2 0.2 - - + -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 2.9 22.0 + - - +
40A TRP 3.2 2.0 + - - +
42A HIS* 1.3 99.4 + - - +
44A THR* 1.3 57.8 + - - +
45A ASN 3.3 0.9 - - - -
46A ILE* 4.9 0.2 - - - -
119A SER* 4.4 3.1 + - - -
328A VAL* 3.6 3.0 - - - +
329A VAL* 2.9 49.7 + - + +
335A TRP* 3.3 25.8 - - + -
346A LYS* 3.8 21.3 - - + +
----------------------------------------------------------
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 2.8 66.9 + - + +
41A ALA* 3.7 5.9 + - - -
43A ASP* 1.3 77.7 - - + +
45A ASN* 1.3 59.1 + - - +
318A MET* 4.1 17.5 - - + -
326A ARG* 2.6 42.3 + - - -
328A VAL* 3.3 14.4 - - - +
346A LYS* 4.1 7.4 - - + -
----------------------------------------------------------
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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