Contacts of the helix formed by residues 15 - 42 (chain A) in PDB entry 6B3I
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 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 3.3 7.8 + - - +
14A PHE* 1.3 73.6 - - - +
16A VAL* 1.3 63.5 + - - +
17A ASP* 3.2 13.2 + - - +
18A ARG* 3.1 57.3 + - + +
19A ASP* 3.1 29.7 + - - +
44B ARG* 6.1 0.2 - - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.8 27.7 + - + -
15A ASP* 1.3 70.9 + - - +
17A ASP* 1.3 80.0 + - - +
19A ASP* 3.4 1.2 + - - +
20A ALA* 3.0 23.7 + - - +
51B GLN* 3.6 40.8 - - + +
52B ILE* 4.0 8.1 - - + +
55B LYS* 3.6 24.2 - - + +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.2 8.4 + - - +
16A VAL* 1.3 85.6 - - - +
18A ARG* 1.3 57.3 + - - +
20A ALA* 4.0 4.9 - - - +
21A LYS* 3.0 30.1 + - - +
55B LYS* 3.2 37.3 + - - +
59B THR* 4.6 5.9 + - - +
60B TYR* 5.0 0.5 + - - -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.1 44.2 + - + +
16A VAL 3.2 0.2 - - - -
17A ASP* 1.3 77.9 - - - +
19A ASP* 1.3 60.1 + - - +
21A LYS* 3.3 10.9 + - + +
22A LYS* 2.7 40.2 + - + +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.4 13.0 - - - -
15A ASP* 3.1 19.4 + - - +
16A VAL 4.1 0.2 - - - +
18A ARG* 1.3 82.0 - - - +
20A ALA* 1.3 61.5 + - - +
22A LYS* 3.3 6.0 + - - +
23A LEU* 2.8 34.3 + - - +
40B ILE* 3.6 18.7 - - + +
44B ARG* 2.8 42.0 + - - -
52B ILE* 3.6 20.9 - - + -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL 3.0 17.7 + - - +
17A ASP* 4.0 4.7 - - - +
19A ASP* 1.3 76.9 - - - +
21A LYS* 1.3 57.4 + - - +
23A LEU* 3.3 5.7 + - - +
24A ASN* 2.9 28.9 + - - +
52B ILE* 4.1 26.5 - - + +
55B LYS* 4.5 7.6 - - + +
56B TYR* 3.7 23.6 - - + +
59B THR* 6.0 0.4 - - - +
60B TYR* 3.8 7.4 - - + -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.0 19.7 + - - +
18A ARG* 3.5 10.1 - - + +
20A ALA* 1.3 76.4 - - - +
22A LYS* 1.3 61.9 + - - +
24A ASN* 3.4 2.8 + - - +
25A LYS* 3.0 23.0 + - + +
60B TYR* 3.1 21.4 + - - +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.7 24.6 + - + +
19A ASP* 3.7 8.3 - - - +
21A LYS* 1.3 74.6 - - - +
23A LEU* 1.3 57.2 + - - +
25A LYS* 3.4 12.5 + - + +
26A ALA* 3.0 26.9 + - - +
36B ALA* 3.8 33.3 - - + +
39B GLU* 3.6 25.7 - - - +
40B ILE* 4.1 16.4 - - + +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP 2.8 17.0 + - - +
20A ALA* 3.6 5.6 - - - +
21A LYS 3.2 0.2 - - - -
22A LYS* 1.3 75.6 - - - +
24A ASN* 1.3 59.1 + - - +
26A ALA* 3.1 2.9 + - - +
27A CYS* 2.8 35.2 + - - -
36B ALA 4.6 0.9 - - - +
37B ILE* 4.2 29.8 - - + +
40B ILE* 3.9 33.4 - - + -
41B LEU* 5.4 7.4 - - + -
52B ILE* 3.8 27.6 - - + -
56B TYR* 4.3 9.9 - - + -
64B LEU* 3.8 28.5 - - + -
68B LEU* 6.3 1.3 - - + -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 2.9 14.4 + - - +
21A LYS 3.4 3.7 + - - +
23A LEU* 1.3 76.5 - - - +
25A LYS* 1.3 57.5 + - - +
27A CYS* 4.4 0.2 - - - -
28A LYS* 3.0 50.0 + - - +
56B TYR* 3.2 34.9 + - + -
60B TYR* 3.5 41.0 - - + +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.0 18.1 + - + +
22A LYS* 3.6 12.1 - - + +
24A ASN* 1.3 80.4 + - - +
26A ALA* 1.3 57.1 + - - +
28A LYS* 3.6 4.2 + - - +
29A GLY* 3.0 24.6 + - - -
33B ASN* 4.1 5.9 + - - +
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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 LYS 3.0 17.0 + - - +
23A LEU* 3.1 5.8 + - - +
25A LYS* 1.3 77.8 - - - +
27A CYS* 1.3 62.0 + - - +
29A GLY 3.5 0.2 + - - -
30A MET* 3.1 29.4 + - - +
33B ASN* 3.4 37.7 - - + +
36B ALA* 3.9 12.6 - - + -
37B ILE* 3.8 14.1 - - + -
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Residues in contact with CYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.8 26.9 + - - +
24A ASN 4.0 3.4 - - - +
26A ALA* 1.3 71.5 - - - +
28A LYS* 1.3 67.6 + - - +
30A MET* 3.3 1.6 + - - -
31A GLY 3.2 6.8 + - - -
37B ILE* 4.9 7.6 - - - -
56B TYR* 4.1 11.2 - - - +
64B LEU* 4.4 9.6 - - - -
67B VAL* 3.8 26.2 - - + -
68B LEU* 3.8 29.2 - - - -
71B GLU* 2.8 31.5 - - - +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.0 43.2 + - - +
25A LYS* 4.1 4.0 - - - +
27A CYS* 1.3 82.9 - - - +
29A GLY* 1.3 61.5 + - - +
31A GLY* 3.4 2.3 + - - +
32A THR* 3.0 26.7 + - - -
56B TYR* 4.4 3.0 + - - -
62B LYS* 4.9 18.5 - - - +
67B VAL* 4.5 14.3 - - - +
71B GLU* 4.7 7.0 + - - -
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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 LYS 3.0 16.5 + - - -
26A ALA 3.5 0.2 + - - -
27A CYS 3.2 0.4 - - - -
28A LYS* 1.3 77.3 - - - +
30A MET* 1.3 57.1 + - - +
32A THR* 3.3 6.7 + - - -
33A ASN* 2.8 35.1 + - - -
33B ASN* 3.1 21.1 - - - -
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 17.4 + - - +
27A CYS 3.3 0.2 + - - -
29A GLY* 1.3 73.2 - - - +
31A GLY* 1.3 61.4 + - - +
33A ASN* 4.2 4.0 - - - +
34A GLU* 2.9 40.6 + - - +
30B MET* 3.6 33.4 - - + +
33B ASN* 3.5 15.7 - - + +
34B GLU* 3.7 25.4 - - + +
37B ILE* 3.9 15.3 - - + -
71B GLU* 3.8 36.3 - - + +
72B LEU* 3.8 21.8 - - + -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A CYS 3.2 11.3 + - - -
28A LYS* 3.4 4.0 + - - -
29A GLY 3.3 0.2 - - - -
30A MET* 1.3 78.2 - - - +
32A THR* 1.3 59.6 + - - +
34A GLU* 4.1 5.4 - - - +
35A ALA* 3.1 24.1 + - - +
309A LYS* 5.1 3.1 + - - -
71B GLU* 3.5 18.2 + - - -
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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 LYS* 3.0 17.4 + - - +
29A GLY* 3.3 6.9 + - - -
31A GLY* 1.3 73.6 - - - +
33A ASN* 1.3 71.7 + - - +
35A ALA* 3.2 7.7 + - - +
36A ALA* 3.0 22.0 + - + +
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Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 2.8 27.1 + - - +
30A MET* 4.3 0.2 - - - +
32A THR* 1.3 78.9 - - - +
34A GLU* 1.3 62.1 + - - +
36A ALA* 3.3 2.5 + - - -
37A ILE* 3.1 28.1 + - - +
25B LYS* 4.2 3.6 - - - +
26B ALA* 3.4 38.1 - - - +
29B GLY* 3.1 20.2 - - - -
30B MET* 3.4 15.3 - - - +
33B ASN* 3.0 22.8 - - - +
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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
----------------------------------------------------------
30A MET* 2.9 33.4 + - - +
31A GLY* 4.1 3.5 - - - +
33A ASN* 1.3 73.0 - - - +
35A ALA* 1.3 61.4 + - - +
37A ILE* 3.1 8.1 + - - +
38A ILE* 2.8 41.7 + - + +
72A LEU* 5.3 0.8 - - + +
76A PHE* 4.5 16.1 - - + -
306A ASP* 3.4 28.9 - - - +
309A LYS* 6.3 0.2 - - - +
30B MET* 4.0 18.3 - - + +
70B SER 4.4 0.3 - - - +
71B GLU* 2.7 41.0 - - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.1 19.8 + - - +
32A THR* 3.2 7.8 + - - +
34A GLU* 1.3 76.0 - - - +
36A ALA* 1.3 56.2 + - - +
38A ILE* 3.9 4.5 - - - +
39A GLU* 3.0 31.7 + - - +
309A LYS* 4.2 22.1 - - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.0 13.4 + - + +
33A ASN* 3.6 9.0 - - - +
34A GLU 3.2 0.4 - - - -
35A ALA* 1.3 77.9 - - - +
37A ILE* 1.3 59.8 + - - +
39A GLU* 3.5 3.1 + - - +
40A ILE* 3.4 28.8 + - - +
22B LYS* 3.9 28.7 + - + +
23B LEU* 5.0 1.3 - - - -
26B ALA* 4.0 15.9 - - + -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN 3.1 16.9 + - - +
34A GLU* 3.1 7.8 + - - +
36A ALA* 1.3 73.7 - - - +
38A ILE* 1.3 61.0 + - - +
40A ILE* 3.3 2.1 + - - +
41A LEU* 3.0 50.6 + - + +
68A LEU* 4.4 22.4 - - + -
71A GLU* 5.9 0.2 - - - +
72A LEU* 4.5 18.2 - - + -
76A PHE* 4.8 11.7 - - + -
23B LEU* 4.1 18.8 - - + -
26B ALA* 3.9 16.4 - - + -
27B CYS* 4.5 6.3 - - - -
30B MET* 4.4 19.5 - - + -
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 2.8 30.1 + - + +
35A ALA* 4.0 4.3 - - - +
37A ILE* 1.3 72.3 - - - +
39A GLU* 1.3 57.3 + - - +
42A SER* 2.6 36.6 + - - -
76A PHE* 3.6 33.2 - - + -
306A ASP* 4.0 4.3 - - + +
309A LYS* 3.7 39.7 - - + +
310A LEU* 3.7 23.7 - - + +
313A ALA* 3.7 26.7 - - + -
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 3.0 18.6 + - - +
36A ALA* 3.9 3.8 - - - +
37A ILE 3.3 0.4 - - - -
38A ILE* 1.3 77.3 - - - +
40A ILE* 1.3 63.8 + - - +
42A SER* 4.1 3.7 + - - -
43A GLY* 3.2 23.0 + - - -
44A ARG* 4.0 21.6 + - - -
313A ALA* 6.1 0.2 - - - -
22B LYS* 3.1 24.6 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 3.4 10.3 + - - +
37A ILE 3.3 3.9 + - - +
38A ILE 3.2 0.6 - - - -
39A GLU* 1.3 87.9 - - - +
41A LEU* 1.3 70.7 + - + +
42A SER 3.1 3.1 + - - -
44A ARG* 3.3 46.0 + - + +
49A ARG* 5.1 2.8 + - + +
52A ILE* 4.2 12.6 - - + -
19B ASP* 3.3 33.9 - - + +
22B LYS* 3.6 25.8 - - + -
23B LEU* 3.6 31.6 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.0 38.5 + - + +
38A ILE 4.4 1.6 - - - +
40A ILE* 1.3 83.8 - - + +
42A SER* 1.3 55.9 + - - +
44A ARG 4.3 0.6 - - - +
49A ARG* 3.6 28.1 + - + +
64A LEU* 5.7 0.4 - - + -
68A LEU* 5.0 4.7 - - + -
76A PHE* 5.9 0.4 - - + -
80A ALA* 3.7 38.8 - - + +
83A LEU* 3.5 28.7 - - + +
84A LEU* 3.8 31.4 - - + -
310A LEU* 4.4 10.8 - - + -
314A LEU* 4.1 2.8 - - - +
23B LEU* 5.4 8.1 - - + -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE 2.6 22.9 + - - -
39A GLU* 4.1 3.5 + - - -
41A LEU* 1.3 76.6 - - - +
43A GLY* 1.3 60.3 + - - +
44A ARG 3.5 4.3 - - - +
49A ARG* 6.0 0.2 - - - +
310A LEU* 4.7 3.6 - - - -
313A ALA* 3.2 41.0 + - - +
314A LEU* 3.8 17.5 - - - +
316A HIS* 3.3 25.1 + - - -
----------------------------------------------------------
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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