Contacts of the helix formed by residues 25 - 52 (chain B) in PDB entry 2EHO
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 ASN 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 5.2 3.1 + - - -
8B GLU 5.3 1.9 - - - +
9B LEU* 3.0 33.2 - - + +
12B GLU* 3.8 18.6 - - - +
23B ALA 3.4 1.2 + - - -
24B PHE* 1.3 74.9 - - - +
26B GLU* 1.3 64.8 + - - +
27B ASP* 3.8 9.5 - - - +
28B GLY* 3.0 22.5 - - - +
29B LEU* 3.0 21.1 + - - +
79B TYR* 3.0 15.4 + - - +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.3 37.4 + - + +
25B ASN* 1.3 73.2 - - - +
27B ASP* 1.3 63.9 + - - +
29B LEU* 3.3 3.9 + - - +
30B ARG* 3.1 24.3 + - - +
107B ALA* 5.7 1.1 - - + -
109B GLU* 5.7 0.7 - - - +
157H TYR* 4.1 14.0 + - - -
162H SER* 3.2 27.7 + - - -
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 3.2 8.4 - - - +
26B GLU* 1.3 79.8 - - - +
28B GLY* 1.3 63.4 + - - +
30B ARG* 3.2 11.0 + - - +
31B GLN* 3.1 48.1 + - - +
165H VAL* 6.1 1.2 - - - +
166H ALA* 6.0 2.6 - - - +
173H ARG* 4.9 15.4 + - - -
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 4.4 11.5 - - - +
9B LEU* 4.4 5.4 - - - -
25B ASN* 3.0 28.3 - - - +
27B ASP* 1.3 78.3 - - - +
29B LEU* 1.3 54.1 + - - +
31B GLN* 3.3 13.7 + - - +
32B VAL* 2.7 36.9 + - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 4.0 9.2 - - + +
145A ALA* 3.7 29.8 - - + -
9B LEU* 4.3 12.3 - - + +
24B PHE* 3.6 30.7 - - + -
25B ASN 3.0 12.0 + - - +
26B GLU 3.6 9.0 - - - +
28B GLY* 1.3 74.8 - - - +
30B ARG* 1.3 63.5 + - - +
32B VAL* 3.0 9.5 + - + +
33B LEU* 3.0 32.1 + - + +
76B THR* 3.1 29.2 - - - +
79B TYR* 5.8 2.5 - - + -
80B LEU* 4.7 8.1 - - + -
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS* 4.8 19.2 + - - -
26B GLU 3.1 11.3 + - - +
27B ASP* 3.2 14.6 + - - +
29B LEU* 1.3 81.7 - - - +
31B GLN* 1.3 58.9 + - + +
32B VAL 3.2 0.2 + - - -
33B LEU* 3.2 10.8 + - - +
34B GLU* 2.9 66.9 + - + +
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 3.0 45.8 - - + +
27B ASP* 3.1 41.5 + - - +
28B GLY* 3.3 7.1 + - - +
30B ARG* 1.3 75.5 - - + +
32B VAL* 1.3 58.0 + - - +
34B GLU* 4.3 7.5 - - - +
35B GLU* 3.2 33.2 + - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 4.3 9.0 - - + +
6B ALA* 4.0 33.0 - - + +
9B LEU* 4.1 8.5 - - + -
28B GLY 2.7 26.9 - - - +
29B LEU* 3.3 11.9 - - + +
30B ARG 3.0 0.6 - - - -
31B GLN* 1.3 78.0 - - - +
33B LEU* 1.3 61.8 - - + +
35B GLU* 3.4 7.0 - - - +
36B MSE 3.1 27.6 + - + +
72B ASN* 3.7 33.2 - - + +
76B THR* 4.3 12.8 - - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL 5.5 0.7 - - - +
145A ALA* 3.8 21.3 - - + +
148A HIS* 3.5 42.4 - - + +
149A MSE 3.5 33.2 - - + -
150A PRO* 5.4 0.3 - - - +
29B LEU* 3.0 30.5 + - + +
30B ARG* 3.8 9.9 - - - +
32B VAL* 1.3 72.6 - - - +
34B GLU* 1.3 54.9 + - + +
35B GLU 2.7 5.3 + - - -
36B MSE 2.4 40.9 + - - +
37B LYS* 2.9 10.6 + - - +
76B THR* 5.2 4.7 - - + +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG* 2.9 53.1 + - + +
31B GLN* 4.5 5.5 - - - +
33B LEU* 1.3 75.7 - - + +
35B GLU* 1.3 60.4 + - - +
37B LYS* 3.6 20.4 + - + +
38B ALA* 3.2 21.7 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.6 24.6 + - - -
3B CYS* 4.7 4.9 + - - -
4B GLU 5.5 0.2 + - - -
5B LYS* 3.6 29.9 + - - +
31B GLN 3.2 19.2 + - - +
32B VAL* 3.4 8.7 - - - +
33B LEU 2.7 4.2 + - - -
34B GLU* 1.3 75.9 - - - +
36B MSE 1.3 58.7 + - - +
38B ALA* 3.7 5.7 - - + +
39B LEU* 3.0 34.7 + - - +
72B ASN* 4.3 19.2 + - - +
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Residues in contact with MSE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MSE 3.3 39.0 - - + +
150A PRO* 3.7 13.9 - - + -
153A LEU* 4.3 6.5 - - + -
32B VAL* 3.1 17.9 - - - +
33B LEU* 2.4 38.8 + - - +
35B GLU* 1.3 70.8 - - - +
37B LYS* 1.3 54.7 + - - +
39B LEU* 3.1 2.9 + - - -
40B TYR* 2.7 33.1 + - - +
69B LEU* 2.8 52.1 - - + +
72B ASN* 3.9 20.4 - - + +
73B ARG* 3.7 8.7 - - + +
76B THR* 4.8 2.0 - - - -
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS 6.0 3.1 - - - +
150A PRO* 3.9 12.2 - - + +
33B LEU 2.9 8.2 + - - +
34B GLU* 3.7 21.7 - - + +
36B MSE 1.3 76.4 - - - +
38B ALA* 1.3 62.9 + - - +
40B TYR* 3.0 13.7 + - + +
41B GLU* 3.1 41.1 + - + +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU 3.2 14.5 + - - +
35B GLU* 3.7 7.4 - - - +
37B LYS* 1.3 81.8 - - - +
39B LEU* 1.3 64.6 + - + +
40B TYR 3.0 1.4 + - - -
41B GLU* 3.5 8.9 + - - -
42B GLN* 3.2 46.1 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 3.2 51.8 - - + +
35B GLU* 3.0 26.6 + - - +
36B MSE 3.1 5.4 + - - +
38B ALA* 1.3 75.3 - - + +
40B TYR* 1.3 57.3 + - - +
42B GLN* 5.2 0.9 - - - -
43B ASN* 3.0 26.1 + - - +
65B ARG* 3.8 14.4 - - + +
68B SER* 3.3 30.1 - - - -
69B LEU* 3.6 19.9 - - + +
72B ASN* 3.4 21.5 - - - +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PRO* 3.6 24.5 - - + -
151A PRO* 3.8 47.5 + - + +
152A ASN* 5.0 3.6 - - + +
36B MSE 2.7 14.8 + - - +
37B LYS* 3.0 13.3 + - + +
39B LEU* 1.3 72.4 - - - +
41B GLU* 1.3 60.1 + - + +
43B ASN* 2.7 10.6 + - + +
44B GLN* 2.7 69.6 + - + +
69B LEU* 4.6 8.7 - - + -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS* 3.1 35.5 + - + +
38B ALA* 4.2 9.5 - - - +
40B TYR* 1.3 81.1 - - + +
42B GLN* 1.3 60.1 + - + +
43B ASN 2.7 12.3 + - - -
44B GLN* 2.9 11.0 + - - +
45B SER* 2.8 26.9 + - - -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.2 37.9 + - - +
39B LEU* 4.9 1.1 - - - +
41B GLU* 1.3 80.3 + - + +
43B ASN* 1.3 56.3 + - - +
45B SER* 4.4 6.5 - - - -
46B ASP* 3.0 21.9 - - - +
65B ARG* 3.3 24.9 + - - +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 3.0 20.6 + - - +
40B TYR* 2.7 7.1 + - + +
41B GLU 2.7 1.4 + - - -
42B GLN* 1.3 75.2 - - - +
44B GLN* 1.3 65.4 + - - +
45B SER 3.2 1.3 - - - -
46B ASP* 3.6 3.8 + - - +
47B VAL* 2.9 31.4 + - - +
62B ILE* 3.2 35.2 + - - +
65B ARG* 3.0 41.5 + - - +
66B HIS* 4.4 11.7 + - - +
69B LEU* 4.9 3.6 - - + +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 2.7 53.5 + - + +
41B GLU* 3.6 9.4 - - - +
43B ASN* 1.3 75.7 - - - +
45B SER* 1.3 53.9 + - - +
47B VAL* 2.8 15.4 + - + +
48B ASN* 2.8 51.5 + - - +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU 2.8 17.4 + - - -
42B GLN* 4.5 4.3 - - - -
44B GLN* 1.3 75.6 + - - +
46B ASP* 1.3 59.3 + - - +
48B ASN* 2.7 17.0 + - - +
49B GLU* 2.6 38.7 + - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN* 3.0 20.8 - - - +
43B ASN 3.6 5.3 + - - +
44B GLN 3.4 0.4 - - - -
45B SER* 1.3 78.3 + - - +
47B VAL* 1.3 59.5 + - - +
49B GLU* 3.9 9.0 - - - -
50B ALA* 3.2 23.9 + - - +
58B LEU* 3.5 19.1 - - + +
61B THR* 4.3 0.5 - - - +
62B ILE* 3.2 24.3 - - + +
65B ARG* 3.7 17.5 + - - -
42D ARG* 3.4 30.2 + - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN* 2.9 27.7 + - - +
44B GLN* 2.8 19.4 + - + +
46B ASP* 1.3 75.2 - - - +
48B ASN* 1.3 65.1 + - - +
50B ALA* 3.2 6.7 + - - +
51B LYS* 3.1 50.0 + - - +
62B ILE* 3.6 25.1 - - + -
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLN* 2.8 39.6 + - - +
45B SER* 2.7 14.7 + - - +
47B VAL* 1.3 68.5 - - - +
49B GLU* 1.3 53.5 + - - +
50B ALA 2.7 15.6 + - - -
51B LYS* 2.9 28.8 + - - +
52B SER* 3.1 18.5 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 2.6 23.9 + - - +
46B ASP* 3.8 9.6 - - - +
48B ASN* 1.3 71.4 - - - +
50B ALA* 1.3 55.3 + - - +
52B SER* 4.4 1.8 - - - -
53B GLY* 3.1 32.8 - - - +
55B ARG* 3.6 27.0 + - - +
58B LEU* 3.8 5.7 - - - +
42D ARG* 3.3 26.3 + - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP 3.2 17.6 + - - +
47B VAL* 3.2 7.8 + - - +
48B ASN 2.7 2.6 + - - -
49B GLU* 1.3 78.9 - - - +
51B LYS* 1.3 63.6 + - + +
52B SER 3.2 2.0 + - - -
54B GLY* 3.8 18.4 + - - +
55B ARG 3.7 18.4 - - - +
56B SER* 5.2 3.4 - - - -
58B LEU* 4.4 8.1 - - + -
59B ILE* 5.8 6.3 - - + -
62B ILE* 5.9 1.1 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.1 38.5 + - + +
48B ASN* 2.9 17.6 + - - +
50B ALA* 1.3 76.2 - - + +
52B SER* 1.3 59.0 + - - +
54B GLY 4.8 0.2 - - - -
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 3.1 14.5 + - - +
49B GLU* 4.4 1.6 - - - -
51B LYS* 1.3 80.8 - - - +
53B GLY* 1.3 60.6 + - - +
54B GLY* 2.6 19.3 + - - -
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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