Contacts of the helix formed by residues 25 - 52 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J LYS* 6.0 0.2 - - - +
8J GLU* 6.3 1.2 - - - +
9J LEU* 3.1 26.7 - - - +
12J GLU* 4.2 12.6 + - - +
23J ALA* 3.0 8.3 + - + +
24J PHE* 1.3 75.4 - - - +
26J GLU* 1.3 62.8 + - - +
27J ASP* 4.3 4.9 - - + +
28J GLY* 3.5 17.0 - - - +
29J LEU* 3.5 14.0 + - - +
79J TYR* 2.8 28.7 + - - -
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Residues in contact with GLU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PHE* 3.4 24.9 + - + +
25J ASN* 1.3 71.9 - - - +
27J ASP* 1.3 65.6 + - - +
29J LEU* 3.8 3.6 - - - +
30J ARG* 2.9 56.2 + - - +
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Residues in contact with ASP 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J ASN* 3.2 5.3 - - + +
26J GLU* 1.3 84.1 - - - +
28J GLY* 1.3 59.1 + - - +
30J ARG* 2.8 35.1 + - - +
31J GLN* 2.9 39.4 + - - +
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Residues in contact with GLY 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS* 4.3 20.6 - - - +
9J LEU* 4.4 6.7 - - - -
25J ASN* 3.5 22.9 - - - +
26J GLU 3.2 0.4 - - - -
27J ASP* 1.3 74.4 - - - +
29J LEU* 1.3 61.5 + - - +
30J ARG 3.0 2.0 + - - -
31J GLN* 3.2 1.9 + - - +
32J VAL* 2.8 38.2 + - - +
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Residues in contact with LEU 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I VAL* 3.8 27.4 - - + +
145I ALA* 4.5 6.5 - - + -
9J LEU* 4.3 11.8 - - + +
24J PHE* 3.9 26.7 - - + -
25J ASN 3.5 15.3 + - - +
26J GLU* 3.5 6.0 + - - +
28J GLY* 1.3 75.8 - - - +
30J ARG* 1.3 60.9 + - - +
32J VAL* 3.9 4.5 - - + -
33J LEU* 3.2 36.2 + - + +
76J THR* 4.0 32.1 - - + +
79J TYR* 5.5 2.7 - - + -
80J LEU* 4.4 10.1 - - + -
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Residues in contact with ARG 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J GLU* 2.9 46.7 + - - +
27J ASP* 2.8 40.3 + - - +
28J GLY 3.0 0.2 - - - -
29J LEU* 1.3 77.3 - - - +
31J GLN* 1.3 63.7 + - + +
33J LEU* 3.0 9.1 + - + +
34J GLU* 2.8 50.3 + - - +
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Residues in contact with GLN 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS* 3.2 47.3 + - + +
27J ASP* 2.9 30.6 + - - +
28J GLY 3.8 3.4 - - - +
30J ARG* 1.3 78.3 - - + +
32J VAL* 1.3 57.2 + - - +
34J GLU* 3.1 13.9 + - + +
35J GLU* 2.8 33.7 + - + +
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Residues in contact with VAL 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS* 4.2 9.2 - - + +
6J ALA* 4.0 28.9 - - + +
9J LEU* 4.3 9.2 - - + -
28J GLY 2.8 29.6 + - - +
29J LEU* 3.9 7.0 - - + +
31J GLN* 1.3 76.9 - - - +
33J LEU* 1.3 60.1 + - + +
35J GLU* 3.4 7.6 + - - +
36J MSE 3.0 32.0 + - + +
72J ASN* 3.9 24.0 - - + +
76J THR* 3.4 29.2 - - + -
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Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I VAL 4.7 1.6 - - - +
145I ALA* 4.1 14.4 - - + +
148I HIS* 3.8 44.9 - - + +
149I MSE 3.4 34.1 - - + -
150I PRO* 5.5 0.7 - - + +
29J LEU* 3.2 33.5 + - + +
30J ARG* 3.0 8.3 + - + +
32J VAL* 1.3 78.1 - - + +
34J GLU* 1.3 66.3 + - - +
36J MSE 3.7 11.0 - - + +
37J LYS* 3.1 21.8 + - - +
76J THR* 6.1 1.8 - - + +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ARG* 2.8 47.5 + - - +
31J GLN* 3.1 18.1 + - + +
33J LEU* 1.3 75.0 - - - +
35J GLU* 1.3 69.0 + - - +
36J MSE 3.0 0.9 - - - -
37J LYS* 2.6 25.3 + - - +
38J ALA* 2.8 14.5 + - - +
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Residues in contact with GLU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J MSE 3.9 15.8 + - - +
3J CYS* 4.1 5.9 - - - -
4J GLU 4.7 0.7 + - - -
5J LYS* 3.5 31.3 + - - +
31J GLN 2.8 16.8 + - - +
32J VAL* 3.5 10.8 - - - +
34J GLU* 1.3 72.2 - - - +
36J MSE 1.3 53.2 + - - +
38J ALA* 4.2 1.1 - - - -
39J LEU* 2.7 39.5 + - + +
72J ASN* 3.5 27.2 + - - +
1006J SO4 3.0 39.0 + - - +
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Residues in contact with MSE 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I MSE 3.1 54.1 - - + +
150I PRO* 3.9 19.5 - - + -
153I LEU* 4.4 6.7 - - + -
32J VAL* 3.0 23.0 + - - +
33J LEU* 3.7 15.0 - - - +
34J GLU 2.9 0.6 + - - -
35J GLU* 1.3 78.4 - - - +
37J LYS* 1.3 51.9 + - - +
39J LEU* 3.5 2.7 - - - +
40J TYR* 2.7 37.1 + - - +
69J LEU* 3.6 35.8 - - + +
72J ASN* 3.7 28.5 - - + -
73J ARG* 4.1 5.8 - - + -
76J THR* 5.3 1.8 - - - -
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Residues in contact with LYS 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I PRO* 4.3 12.1 - - + +
33J LEU 3.1 13.1 + - - +
34J GLU* 2.6 20.3 + - - +
36J MSE 1.3 72.1 - - - +
38J ALA* 1.3 65.6 + - - +
40J TYR* 3.2 4.3 + - + +
41J GLU* 2.9 53.2 + - + +
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Residues in contact with ALA 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J GLU 2.8 14.5 + - - +
35J GLU* 3.2 9.2 - - - +
37J LYS* 1.3 75.2 - - - +
39J LEU* 1.3 67.4 + - - +
41J GLU* 2.9 20.0 + - - +
42J GLN* 3.0 15.6 + - - +
1006J SO4 3.4 19.7 - - - +
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Residues in contact with LEU 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J MSE 3.4 39.3 - - + -
35J GLU* 2.7 30.8 + - - +
36J MSE 3.5 3.4 - - - +
38J ALA* 1.3 72.6 - - - +
40J TYR* 1.3 57.4 + - - +
42J GLN* 3.6 5.7 + - - +
43J ASN* 3.0 30.8 + - - +
65J ARG* 3.9 25.1 - - + +
68J SER* 3.9 13.0 - - - -
69J LEU* 3.9 19.7 - - + -
72J ASN* 3.7 26.5 - - - +
1006J SO4 3.9 13.4 + - - +
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Residues in contact with TYR 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I PRO* 3.5 28.3 - - + -
151I PRO* 3.6 42.5 - - + +
152I ASN* 4.8 6.3 + - - -
153I LEU* 5.7 1.3 - - + -
36J MSE 2.7 20.2 + - - +
37J LYS* 3.5 6.3 - - + +
39J LEU* 1.3 72.0 - - - +
41J GLU* 1.3 74.7 + - + +
43J ASN* 3.3 4.2 + - + +
44J GLN* 3.0 57.4 + - + +
69J LEU* 4.3 17.2 - - + +
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Residues in contact with GLU 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LYS* 2.9 48.6 + - + +
38J ALA* 2.9 13.9 + - - +
40J TYR* 1.3 84.8 - - + +
42J GLN* 1.3 65.2 + - - +
44J GLN* 3.1 9.3 + - - +
45J SER* 3.0 22.6 + - - -
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Residues in contact with GLN 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ALA 3.0 16.2 + - - +
39J LEU* 3.9 4.5 - - - +
41J GLU* 1.3 76.6 - - - +
43J ASN* 1.3 62.9 + - - +
45J SER* 3.5 10.6 + - - -
46J ASP* 2.8 47.2 + - - +
65J ARG* 3.5 27.3 - - - +
42L ARG* 4.3 7.1 - - - +
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Residues in contact with ASN 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J LEU 3.0 15.6 + - - +
40J TYR* 3.6 10.1 - - + +
41J GLU 3.1 0.2 - - - -
42J GLN* 1.3 74.1 - - - +
44J GLN* 1.3 70.2 + - + +
46J ASP* 3.0 5.5 + - - +
47J VAL* 2.7 28.8 + - + +
62J ILE* 3.4 36.0 + - - +
65J ARG* 2.7 46.8 + - - +
66J HIS* 4.2 19.4 + - - +
69J LEU* 5.0 4.7 - - + +
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Residues in contact with GLN 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J TYR* 3.0 51.8 + - + +
41J GLU* 3.4 9.4 - - - +
43J ASN* 1.3 78.5 - - - +
45J SER* 1.3 66.4 - - - +
47J VAL* 3.1 22.9 + - - +
48J ASN* 3.1 24.0 + - - +
51J LYS* 5.9 0.5 + - - -
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Residues in contact with SER 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J GLU 3.0 12.0 + - - -
42J GLN* 3.6 17.7 + - - -
44J GLN* 1.3 74.3 - - - +
46J ASP* 1.3 64.1 + - - +
48J ASN* 2.8 24.6 + - - +
49J GLU* 3.3 19.8 + - - +
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Residues in contact with ASP 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J GLN* 2.8 26.6 + - - +
43J ASN 3.0 8.3 + - - +
45J SER* 1.3 82.8 + - - +
47J VAL* 1.3 61.7 + - - +
49J GLU* 3.1 8.9 + - - +
50J ALA* 3.0 19.8 + - - +
58J LEU* 3.5 28.4 - - + +
61J THR* 4.2 2.6 - - - +
62J ILE* 4.0 16.4 - - + -
65J ARG* 2.8 29.2 + - - +
42L ARG* 3.1 24.1 + - - +
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Residues in contact with VAL 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J ASN* 2.7 39.8 + - + +
44J GLN* 3.4 20.0 - - - +
45J SER 3.0 0.2 + - - -
46J ASP* 1.3 72.9 - - - +
48J ASN* 1.3 60.0 + - - +
50J ALA* 3.3 4.1 - - + +
51J LYS* 3.1 42.3 + - + +
62J ILE* 3.9 31.2 - - + -
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Residues in contact with ASN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLN* 3.1 22.8 + - - +
45J SER* 2.8 10.2 + - - +
47J VAL* 1.3 76.7 - - - +
49J GLU* 1.3 66.5 + - - +
50J ALA 2.9 2.3 + - - -
51J LYS* 3.3 31.4 + - - +
52J SER* 3.0 33.8 + - - +
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Residues in contact with GLU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J SER* 3.3 20.6 + - - +
46J ASP* 3.1 10.7 + - - +
48J ASN* 1.3 78.1 - - + +
50J ALA* 1.3 58.0 + - - +
52J SER 4.8 1.3 - - - -
53J GLY* 3.0 33.5 - - - -
55J ARG* 3.6 19.9 + - + +
58J LEU* 3.7 9.6 - - + -
42L ARG* 3.3 36.0 + - - -
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Residues in contact with ALA 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ASP 3.0 11.2 + - - +
47J VAL* 3.3 15.5 - - + +
48J ASN 2.9 1.2 - - - -
49J GLU* 1.3 78.0 - - - +
51J LYS* 1.3 67.2 + - + +
54J GLY* 3.7 12.3 + - - -
55J ARG 3.8 17.7 + - - +
56J SER* 4.3 16.9 + - - -
58J LEU* 5.0 1.3 - - + -
59J ILE* 4.6 10.5 - - + -
62J ILE* 4.4 11.4 - - + -
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Residues in contact with LYS 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLN* 5.9 0.8 + - - -
47J VAL* 3.1 31.9 + - + +
48J ASN* 3.3 37.9 + - - +
50J ALA* 1.3 81.6 - - + +
52J SER* 1.3 64.1 + - - +
53J GLY 3.3 4.1 + - - -
54J GLY* 4.1 2.9 + - - -
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Residues in contact with SER 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J ASN* 3.0 20.7 + - - +
49J GLU* 4.8 1.4 - - - -
51J LYS* 1.3 76.1 - - - +
53J GLY* 1.3 56.4 + - - +
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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