Contacts of the helix formed by residues 28 - 50 (chain o) in PDB entry 3J7Y
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 SER 28 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2154A A 2.9 53.3 + - - -
2155A A 4.9 11.7 - - - -
42I PHE* 5.4 0.4 - - - -
26o PHE 3.4 4.9 + - - -
27o VAL* 1.3 77.4 - - - +
29o LEU* 1.3 64.5 + - - +
30o ARG* 3.8 4.2 + - - -
31o ALA* 3.3 20.3 + - - +
32o LYS* 3.4 24.6 + - - +
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Residues in contact with LEU 29 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156A A 5.4 12.4 + - - +
28o SER* 1.3 72.4 - - - +
30o ARG* 1.3 61.3 + - - +
32o LYS* 3.2 18.9 + - + +
33o GLN* 2.9 54.4 + - + +
191r PRO* 5.6 12.1 - - + -
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Residues in contact with ARG 30 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2153A A 3.6 68.0 + - + +
2154A A 2.9 97.7 + - + +
2247A C 5.9 2.4 - - - +
2248A U 5.5 1.4 + - - -
28o SER* 3.8 5.5 + - - +
29o LEU* 1.3 79.3 - - - +
31o ALA* 1.3 58.8 + - - +
33o GLN* 3.2 15.4 + - - +
34o ASN* 2.9 35.6 + - - +
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Residues in contact with ALA 31 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2153A A 3.7 36.7 + - - +
2154A A 4.6 0.4 - - - +
42I PHE* 4.5 4.7 - - + -
46I LYS* 3.9 14.3 - - + +
27o VAL* 4.4 3.6 - - + -
28o SER* 3.3 25.2 + - - +
29o LEU 3.2 0.2 - - - -
30o ARG* 1.3 79.3 - - - +
32o LYS* 1.3 58.1 + - - +
34o ASN* 3.2 5.1 + - - +
35o MET* 2.9 31.4 + - - +
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Residues in contact with LYS 32 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LYS* 5.8 0.7 - - - -
49I ALA* 3.5 39.3 + - + +
50I VAL* 4.3 10.5 - - + +
52I GLU* 4.8 8.9 + - - -
27o VAL* 3.9 16.8 - - + -
28o SER 3.4 13.4 + - - +
29o LEU* 3.2 24.2 + - + +
31o ALA* 1.3 79.9 - - - +
33o GLN* 1.3 58.2 + - + +
35o MET* 3.2 8.8 + - - +
36o ILE* 2.9 43.6 + - + +
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Residues in contact with GLN 33 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2245A A 5.8 5.5 + - - -
29o LEU* 2.9 42.0 + - + +
30o ARG* 3.4 15.1 - - - +
32o LYS* 1.3 75.5 - - + +
34o ASN* 1.3 61.2 + - - +
36o ILE* 3.2 11.1 + - + +
37o ARG* 2.9 44.8 + - - +
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Residues in contact with ASN 34 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152A A 3.0 38.7 + - - +
2153A A 3.0 50.3 + - - +
30o ARG* 2.9 18.6 + - - +
31o ALA 3.3 7.6 - - - +
33o GLN* 1.3 77.7 - - - +
35o MET* 1.3 62.1 + - - +
37o ARG* 3.0 37.0 + - - +
38o ARG* 3.1 17.8 + - - +
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Residues in contact with MET 35 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLN* 5.3 1.6 - - - +
46I LYS* 4.1 31.6 - - + +
47I LEU* 3.7 41.7 - - + +
50I VAL* 3.7 19.3 - - + -
218N ILE* 5.5 0.2 - - + -
224N LEU* 4.2 23.3 - - + -
226N ILE* 4.5 9.0 - - + -
31o ALA 2.9 14.7 + - - +
32o LYS* 3.4 9.6 - - - +
34o ASN* 1.3 76.6 - - - +
36o ILE* 1.3 59.2 + - - +
38o ARG* 3.2 19.2 + - - +
39o LEU* 2.9 43.6 + - + +
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Residues in contact with ILE 36 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I VAL* 4.4 23.8 - - + +
211N ASN* 6.1 1.3 - - - +
213N TRP* 4.0 17.5 - - + +
32o LYS* 2.9 35.9 + - + +
33o GLN* 3.6 9.9 - - + +
35o MET* 1.3 77.4 - - - +
37o ARG* 1.3 55.6 + - - +
39o LEU* 3.2 9.2 + - - +
40o GLU* 2.9 49.2 + - - +
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Residues in contact with ARG 37 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2151A A 2.8 36.3 + - - -
2152A A 5.2 3.4 - - - +
33o GLN* 2.9 27.8 + - - +
34o ASN* 3.0 41.0 + - - +
36o ILE* 1.3 77.2 - - - +
38o ARG* 1.3 58.2 + - + +
40o GLU* 3.2 19.1 + - - +
41o ILE* 2.9 39.2 + - + +
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Residues in contact with ARG 38 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2138A U 5.0 5.0 + - - -
2152A A 3.0 47.6 + - - +
2153A A 4.2 2.0 + - - -
43I GLN* 5.4 5.7 - - - +
46I LYS* 3.8 21.8 - - - +
224N LEU* 3.6 27.8 - - + +
72Z ILE* 5.8 6.3 - - + -
73Z LYS* 3.5 38.5 - - - +
115Z HIS 6.1 0.4 - - - -
34o ASN* 3.1 19.7 + - - +
35o MET* 3.4 16.9 - - - +
37o ARG* 1.3 79.0 - - + +
39o LEU* 1.3 57.4 + - - +
41o ILE* 3.2 13.3 + - + +
42o GLU* 2.9 38.5 + - - +
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Residues in contact with LEU 39 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I VAL* 3.7 30.3 - - + -
213N TRP* 3.3 33.9 - - + -
218N ILE* 3.6 33.4 - - + -
223N MET* 3.6 16.6 - - + +
224N LEU* 3.3 27.8 - - + -
35o MET* 2.9 24.0 + - + +
36o ILE* 3.2 10.5 + - - +
38o ARG* 1.3 77.2 - - - +
40o GLU* 1.3 58.0 + - - +
42o GLU* 3.2 6.3 + - - +
43o ALA 2.9 24.6 + - - -
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Residues in contact with GLU 40 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213N TRP* 3.7 20.3 + - + -
55Z LYS* 5.8 5.8 + - - +
56Z TYR* 4.4 2.1 + - - -
36o ILE* 2.9 35.3 + - - +
37o ARG* 3.2 21.3 + - - +
39o LEU* 1.3 77.3 - - - +
41o ILE* 1.3 63.0 - - + +
43o ALA* 3.2 6.2 + - - +
44o GLU* 3.1 21.8 + - - +
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Residues in contact with ILE 41 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Z ILE* 3.8 24.7 - - + -
117Z ILE 4.5 0.2 - - - +
118Z ARG* 3.8 54.5 - - + +
37o ARG* 2.9 24.9 + - + +
38o ARG* 3.2 14.8 + - + +
40o GLU* 1.3 76.0 - - + +
42o GLU* 1.3 62.2 + - + +
44o GLU* 3.2 12.1 + - - +
45o ASN* 2.9 36.5 + - - +
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Residues in contact with GLU 42 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223N MET* 3.0 22.8 - - + +
224N LEU* 2.5 54.7 + - - +
72Z ILE* 6.4 0.4 - - + -
114Z LYS* 4.2 17.5 - - + +
115Z HIS* 3.5 25.8 + - - +
117Z ILE 5.5 0.2 - - - +
38o ARG* 2.9 20.9 + - - +
39o LEU* 3.2 5.4 + - - +
41o ILE* 1.3 80.1 - - + +
43o ALA* 1.3 54.8 + - - +
45o ASN* 3.2 9.6 + - - +
46o HIS* 2.9 39.5 + - + +
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Residues in contact with ALA 43 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213N TRP* 4.0 15.9 - - + -
217N ARG* 4.3 14.4 - - - +
223N MET* 4.2 4.0 - - - +
55Z LYS* 5.2 4.3 - - - +
56Z TYR* 3.7 12.9 - - - +
39o LEU 2.9 12.7 + - - +
40o GLU* 3.2 10.1 + - - +
42o GLU* 1.3 74.9 - - - +
44o GLU* 1.3 57.6 + - - +
46o HIS* 3.2 10.6 + - - +
47o TYR* 2.9 28.9 + - - +
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Residues in contact with GLU 44 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z TYR* 3.5 36.8 + - + -
118Z ARG* 4.4 13.0 + - - +
119Z ILE 4.7 2.3 - - - +
120Z LYS* 3.4 29.8 + - - +
40o GLU 3.1 9.3 + - - +
41o ILE* 3.4 12.4 - - - +
43o ALA* 1.3 80.0 - - - +
45o ASN* 1.3 57.5 + - - +
47o TYR* 3.2 4.6 + - - +
48o TRP* 2.9 57.0 + - + +
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Residues in contact with ASN 45 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Z LYS* 3.2 19.1 + - + +
117Z ILE* 2.4 32.3 + - - +
118Z ARG* 3.4 5.1 - - - +
119Z ILE* 2.6 43.7 + - + +
41o ILE* 2.9 20.2 + - - +
42o GLU* 3.2 12.4 - - - +
44o GLU* 1.3 77.3 - - - +
46o HIS* 1.3 58.2 + - - +
48o TRP* 3.2 9.5 + - - +
49o LEU* 2.9 36.9 + - + +
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Residues in contact with HIS 46 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221N ALA* 3.7 14.6 + - + +
223N MET* 4.6 16.8 - - + +
45Z VAL* 3.2 38.4 - - + +
46Z PHE* 3.7 22.5 - + - -
114Z LYS* 3.2 44.2 + - + +
42o GLU* 2.9 26.4 + - + +
43o ALA* 3.2 12.9 + - - +
45o ASN* 1.3 76.7 - - - +
47o TYR* 1.3 53.7 + - - +
49o LEU* 3.2 5.1 + - - +
50o SER* 2.7 36.6 + - - -
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Residues in contact with TYR 47 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Z ALA* 3.7 29.4 - - + +
52Z ASP* 4.1 10.5 - - + +
53Z HIS* 3.1 27.9 + + - -
56Z TYR* 3.3 50.7 - + + -
58Z GLY* 2.8 34.1 + - - -
43o ALA 2.9 13.5 + - - +
44o GLU 3.2 8.5 + - - +
46o HIS* 1.3 75.9 - - - +
48o TRP* 1.3 95.9 + + - +
50o SER* 3.1 23.3 - - - -
51o MET* 3.2 13.7 + - + +
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Residues in contact with TRP 48 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z TYR* 4.8 2.2 - + + -
57Z GLY* 4.4 8.7 - - - -
58Z GLY* 3.5 32.1 - - - -
64Z HIS* 3.7 25.4 + + + +
67Z HIS* 4.4 4.4 + - - -
102Z ASN* 5.2 0.2 - - - +
119Z ILE* 3.1 40.6 + - + -
120Z LYS* 4.1 3.5 - - - +
121Z PRO* 3.4 42.4 - - + +
123Z LYS* 6.4 0.2 - - - -
44o GLU* 2.9 43.7 + - + +
45o ASN 3.5 7.6 - - - +
47o TYR* 1.3 103.7 - + - +
49o LEU* 1.3 62.6 + - - +
50o SER 3.4 0.2 + - - -
51o MET* 3.5 30.0 - - - +
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Residues in contact with LEU 49 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Z PHE* 3.7 30.1 - - + -
67Z HIS* 4.3 9.2 - - + -
102Z ASN* 4.7 0.3 - - - +
107Z ASN* 3.8 55.0 + - + +
110Z LEU* 3.9 13.0 - - + -
111Z LYS* 3.9 15.7 + - + +
114Z LYS* 4.4 15.9 - - + -
119Z ILE* 3.9 18.2 - - + -
45o ASN 2.9 21.4 + - - +
46o HIS* 3.4 7.2 - - - +
48o TRP* 1.3 76.0 - - - +
50o SER* 1.3 58.9 + - - +
51o MET* 2.8 13.5 + - - -
52o PRO* 4.0 3.3 - - - +
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Residues in contact with SER 50 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Z VAL 4.9 0.7 + - - -
46Z PHE* 3.8 32.0 - - - +
47Z GLN* 3.8 2.9 + - - -
48Z ALA* 3.9 28.6 + - - +
46o HIS 2.7 22.8 + - - -
47o TYR* 3.1 17.4 + - - -
49o LEU* 1.3 74.9 - - - +
51o MET* 1.3 56.0 + - - +
52o PRO* 3.2 11.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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