Contacts of the helix formed by residues 15 - 44 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY 3.3 6.5 + - - +
14B PHE* 1.3 74.3 - - - +
16B VAL* 1.3 62.6 + - - +
17B ASP* 3.1 23.5 + - - +
18B ARG* 3.2 48.1 + - + +
19B ASP* 3.2 25.7 + - - -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.8 31.0 - - + +
52A ILE* 3.9 9.4 - - + +
55A LYS* 3.7 32.3 - - + +
14B PHE* 3.7 26.7 + - + +
15B ASP* 1.3 74.2 + - - +
17B ASP* 1.3 76.9 + - - +
19B ASP* 4.1 1.3 - - - +
20B ALA* 3.1 23.7 + - - +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.2 31.4 + - - +
59A THR* 5.1 2.8 + - - -
15B ASP* 3.1 10.8 + - - +
16B VAL* 1.3 88.0 - - - +
18B ARG* 1.3 63.9 + - + +
20B ALA* 4.0 4.2 - - - +
21B LYS* 3.2 24.6 + - - +
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 5.0 7.5 - - - +
13B GLY 4.8 6.1 + - - -
15B ASP* 3.2 46.1 + - - +
17B ASP* 1.3 77.0 - - + +
19B ASP* 1.3 76.2 + - - +
21B LYS* 3.1 15.8 + - + +
22B LYS* 3.2 26.1 + - - +
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.3 24.4 - - + +
44A ARG* 2.6 48.9 + - - -
52A ILE* 3.6 21.3 - - + +
14B PHE* 3.5 16.6 - - - -
15B ASP 3.2 13.8 + - - +
16B VAL 4.2 1.3 - - - +
18B ARG* 1.3 89.5 + - - +
20B ALA* 1.3 62.3 + - - +
22B LYS* 3.5 3.8 - - - +
23B LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.8 30.2 - - + +
55A LYS* 4.4 9.9 - - + -
56A TYR* 3.5 19.7 - - + +
59A THR* 5.9 0.2 - - - +
60A TYR* 3.5 17.5 - - + -
16B VAL 3.1 19.6 + - - +
17B ASP* 4.3 2.5 - - - +
19B ASP* 1.3 77.1 - - - +
21B LYS* 1.3 59.9 + - - +
23B LEU* 4.0 3.6 - - - -
24B ASN 3.4 13.2 + - - -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.3 19.7 - - - +
17B ASP 3.2 18.9 + - - +
18B ARG* 3.1 8.2 + - + +
19B ASP 3.1 0.8 - - - -
20B ALA* 1.3 76.9 - - - +
22B LYS* 1.3 61.9 + - - +
23B LEU 3.2 0.2 - - - -
24B ASN* 3.1 7.4 + - - +
25B LYS* 2.9 26.3 + - + +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.9 31.3 + - + +
39A GLU* 3.1 25.6 + - - +
40A ILE* 3.6 20.9 - - + -
44A ARG* 5.9 0.9 - - - +
18B ARG* 3.2 22.6 + - - +
19B ASP* 3.5 11.9 - - - +
21B LYS* 1.3 75.9 - - - +
23B LEU* 1.3 63.4 + - - +
25B LYS* 3.7 14.3 - - + +
26B ALA* 2.8 30.0 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 4.6 0.9 - - - +
37A ILE* 4.1 37.2 - - + +
40A ILE* 3.6 29.6 - - + -
41A LEU* 5.4 6.7 - - + -
52A ILE* 3.7 28.5 - - + -
56A TYR* 4.2 6.5 - - + -
64A LEU* 3.8 26.2 - - + -
68A LEU* 6.2 1.1 - - + -
19B ASP 3.1 17.6 + - - +
20B ALA* 4.0 5.4 - - - +
22B LYS* 1.3 77.2 - - - +
24B ASN* 1.3 58.0 + - - +
26B ALA* 3.3 1.9 + - - +
27B CYS* 2.8 39.5 + - - -
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.3 32.9 + - + -
60A TYR* 3.3 47.3 + - + +
20B ALA 3.4 3.4 + - - +
21B LYS* 3.1 11.0 + - - +
23B LEU* 1.3 79.0 - - - +
25B LYS* 1.3 63.8 + - - +
27B CYS* 3.9 0.2 - - - +
28B LYS* 3.0 52.4 + - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 4.2 3.2 - - - +
21B LYS* 2.9 16.5 + - + +
22B LYS* 3.7 12.8 - - + +
23B LEU 3.3 0.2 - - - -
24B ASN* 1.3 79.2 - - - +
26B ALA* 1.3 63.3 + - - +
28B LYS* 3.9 3.0 - - - +
29B GLY* 3.0 19.4 + - - -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 3.4 39.7 - - - +
36A ALA* 4.0 12.6 - - + -
37A ILE* 3.9 12.1 - - + -
22B LYS 2.8 22.9 + - - +
23B LEU* 3.8 4.0 - - - +
25B LYS* 1.3 71.8 - - - +
27B CYS* 1.3 60.0 + - - +
29B GLY 3.1 1.2 + - - -
30B MET* 2.9 32.9 + - - +
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Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.5 8.5 - - - -
56A TYR* 4.2 6.5 - - - +
64A LEU* 4.5 10.3 - - - -
67A VAL* 3.8 22.0 - - + -
68A LEU* 3.6 30.5 - - - -
71A GLU* 2.8 35.6 - - - +
23B LEU* 2.8 31.5 + - - +
24B ASN 3.9 3.4 - - - +
26B ALA* 1.3 73.8 - - - +
28B LYS* 1.3 58.7 + - + +
30B MET* 3.0 16.4 + - - -
31B GLY 3.2 0.5 + - - -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 5.3 1.3 - - - +
62A LYS* 4.8 15.9 - - - +
71A GLU* 4.6 2.2 - - - -
24B ASN* 3.0 41.0 + - - +
25B LYS* 3.9 4.0 - - - +
27B CYS* 1.3 76.6 - - + +
29B GLY* 1.3 59.3 + - - +
31B GLY* 3.8 2.7 + - - +
32B THR* 3.1 26.0 + - - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 3.1 19.1 - - - -
25B LYS 3.0 15.2 + - - -
26B ALA 3.1 2.0 + - - -
28B LYS* 1.3 75.7 - - - +
30B MET* 1.3 63.8 + - - +
32B THR* 3.3 6.3 + - - -
33B ASN* 2.9 30.9 + - - -
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Residues in contact with MET 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.6 31.0 - - + +
33A ASN* 3.4 21.7 - - + +
34A GLU* 4.0 22.2 - - + +
37A ILE* 4.4 9.6 - - + -
71A GLU* 3.4 21.3 - - + +
72A LEU* 3.6 28.7 - - + -
26B ALA 2.9 22.3 + - - +
27B CYS* 3.0 8.7 + - - +
29B GLY* 1.3 77.7 - - - +
31B GLY* 1.3 56.9 + - - +
33B ASN* 3.9 3.0 - - - +
34B GLU* 2.9 46.0 + - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.6 17.1 + - - -
27B CYS 3.2 8.3 + - - -
28B LYS* 3.8 3.3 + - - -
29B GLY 3.3 0.2 - - - -
30B MET* 1.3 78.0 - - - +
32B THR* 1.3 57.3 + - - +
34B GLU* 4.0 5.4 - - - +
35B ALA* 3.0 29.8 + - - +
309B LYS* 4.5 8.8 + - - -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS 3.1 18.6 + - - -
29B GLY* 3.3 8.2 + - - -
30B MET 3.3 0.6 - - - -
31B GLY* 1.3 75.6 - - - +
33B ASN* 1.3 70.5 + - - +
35B ALA* 3.3 7.6 + - - +
36B ALA* 3.1 20.7 + - + +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.1 5.4 + - - +
26A ALA* 3.4 38.0 - - - +
29A GLY* 3.1 21.2 - - - -
30A MET* 3.3 11.9 - - + +
33A ASN* 3.0 22.0 - - - +
29B GLY* 2.9 20.3 + - - +
30B MET 4.0 0.7 - - - +
32B THR* 1.3 80.7 - - - +
34B GLU* 1.3 61.1 + - - +
36B ALA* 3.0 6.3 + - - +
37B ILE* 2.9 32.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.7 21.6 - - + +
70A SER 4.3 0.7 - - - +
71A GLU* 2.8 37.2 - - - +
30B MET* 2.9 37.9 + - - +
31B GLY* 4.1 4.8 - - - +
33B ASN* 1.3 75.2 - - - +
35B ALA* 1.3 53.1 + - - +
37B ILE* 3.7 8.8 - - - +
38B ILE* 2.7 46.6 + - + +
72B LEU* 5.4 0.3 - - - +
76B PHE* 4.4 16.9 - - + -
306B ASP* 3.5 25.5 - - - +
309B LYS* 6.2 2.0 - - + +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY 3.0 21.2 + - - +
32B THR* 3.5 7.6 - - - +
34B GLU* 1.3 76.6 - - - +
36B ALA* 1.3 57.0 + - - +
38B ILE* 3.8 6.3 - - - +
39B GLU* 2.8 30.0 + - - +
309B LYS* 4.2 21.2 - - - +
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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
----------------------------------------------------------
22A LYS* 3.8 30.2 - - + +
23A LEU* 5.0 0.9 - - - -
26A ALA* 3.9 15.7 - - + -
32B THR* 3.1 12.8 + - + +
33B ASN* 3.0 9.9 + - - +
35B ALA* 1.3 75.5 - - - +
37B ILE* 1.3 65.3 + - - +
39B GLU* 3.3 4.1 + - - +
40B ILE* 3.0 30.5 + - - +
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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
----------------------------------------------------------
23A LEU* 4.2 17.9 - - + -
26A ALA* 3.8 20.9 - - + +
27A CYS* 4.9 4.3 - - - +
30A MET* 3.9 29.6 - - + -
33B ASN 2.9 18.0 + - - +
34B GLU* 3.7 8.5 - - - +
36B ALA* 1.3 76.7 - - - +
38B ILE* 1.3 62.1 + - - +
40B ILE* 3.2 2.1 + - - +
41B LEU* 2.9 51.4 + - + +
68B LEU* 4.5 22.7 - - + -
72B LEU* 4.7 12.1 - - + -
76B PHE* 4.7 11.9 - - + -
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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 GLU* 2.7 28.6 + - + +
35B ALA* 3.9 4.7 - - - +
37B ILE* 1.3 72.3 - - - +
39B GLU* 1.3 57.4 + - - +
42B SER* 2.4 36.4 + - - +
76B PHE* 3.7 28.5 - - + -
306B ASP* 3.9 2.7 - - + +
309B LYS* 3.7 33.0 - - + +
310B LEU* 3.7 38.8 - - + +
313B ALA* 3.6 27.6 - - + -
----------------------------------------------------------
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.6 24.0 - - - +
35B ALA 2.8 19.0 + - - +
36B ALA* 3.5 7.6 - - - +
37B ILE 3.2 0.2 - - - -
38B ILE* 1.3 77.4 - - - +
40B ILE* 1.3 61.8 + - + +
42B SER* 3.9 3.6 + - - -
43B GLY* 3.0 28.2 + - - -
44B ARG* 4.1 18.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 3.6 31.0 - - + +
22A LYS* 4.1 27.8 - - + +
23A LEU* 3.9 40.2 - - + -
36B ALA 3.0 18.1 + - - +
37B ILE 3.2 3.1 + - - +
39B GLU* 1.3 77.4 - - + +
41B LEU* 1.3 68.9 + - + +
44B ARG* 3.3 37.5 + - + +
49B ARG* 4.6 2.6 - - + +
52B ILE* 4.0 22.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.4 7.9 - - + -
37B ILE* 2.9 37.9 + - + +
38B ILE 4.3 1.3 - - - +
40B ILE* 1.3 83.8 - - + +
42B SER* 1.3 59.6 + - - +
44B ARG 3.9 2.4 - - - +
49B ARG* 3.3 32.9 + - + +
64B LEU* 5.8 0.4 - - + -
68B LEU* 5.2 4.7 - - + -
76B PHE* 6.0 0.2 - - + -
80B ALA* 3.7 36.8 - - + +
83B LEU* 3.9 22.9 - - + +
84B LEU* 4.0 31.0 - - + -
310B LEU* 4.5 12.8 - - + -
314B LEU* 4.3 1.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE 2.4 27.5 + - - -
39B GLU* 3.9 3.8 + - - -
41B LEU* 1.3 75.7 - - - +
43B GLY* 1.3 59.3 + - - +
44B ARG 3.5 2.7 - - - +
310B LEU* 4.5 3.6 - - - -
313B ALA* 3.4 34.6 + - - +
314B LEU* 3.8 24.9 - - - +
316B HIS* 3.4 24.6 + - - -
----------------------------------------------------------
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 3.0 23.1 + - - -
41B LEU 3.4 0.2 - - - -
42B SER* 1.3 78.5 - - - +
44B ARG* 1.3 82.0 + - - +
48B GLU* 4.5 1.0 - - - +
316B HIS* 5.2 2.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.9 15.5 - - - +
15A ASP 6.1 0.4 - - - +
19A ASP* 2.8 37.6 + - - -
22A LYS* 6.1 0.2 - - - +
39B GLU* 4.1 16.2 + - - +
40B ILE* 3.3 30.9 + - + +
41B LEU 3.9 2.6 - - - +
42B SER 4.7 1.9 - - - +
43B GLY* 1.3 106.6 + - - +
45B THR* 1.3 67.7 + - - +
48B GLU* 3.4 22.7 - - + +
49B ARG* 3.3 26.6 + - + +
52B ILE* 4.0 15.7 - - + -
----------------------------------------------------------
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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