Contacts of the helix formed by residues 36 - 62 (chain E) in PDB entry 2J3W
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 36 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.1 4.7 + - - +
35E GLU* 1.3 82.4 - - - +
37E ASP* 1.3 66.5 + - - +
38E GLU* 2.8 34.0 + - - +
39E ASP* 2.6 58.9 + - - +
40E VAL* 3.4 13.3 + - - +
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Residues in contact with ASP 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E CYS* 4.8 2.8 - - - +
36E ASN* 1.3 75.5 + - - +
38E GLU* 1.3 57.4 + - - +
40E VAL* 3.1 8.6 + - - +
41E ASN* 2.8 35.9 + - - +
121E ASN 4.0 4.4 - - - +
122E HIS* 3.0 54.2 + - - -
124E ALA* 3.9 12.0 + - + -
125E LEU* 3.2 36.2 + - + +
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Residues in contact with GLU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ASN* 2.8 27.1 + - - +
37E ASP* 1.3 73.4 - - - +
39E ASP* 1.3 63.2 + - - +
41E ASN* 3.4 16.3 + - - +
42E LYS* 3.0 37.5 + - + +
124E ALA* 3.9 20.8 - - - +
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Residues in contact with ASP 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.5 33.7 - - + +
35E GLU 5.3 0.5 + - - -
36E ASN* 2.6 43.0 + - - +
38E GLU* 1.3 73.6 - - - +
40E VAL* 1.3 61.8 + - - +
42E LYS* 3.3 20.7 + - - +
43E GLN* 2.8 32.3 + - - +
46E ARG* 4.7 2.5 + - - +
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E VAL* 4.7 3.4 - - + +
30E LEU* 3.8 44.2 - - + +
31E CYS* 3.8 17.5 - - - +
34E TYR* 4.3 9.4 - - + +
36E ASN 3.8 11.7 - - - +
37E ASP* 3.1 11.1 + - - +
39E ASP* 1.3 76.3 - - - +
41E ASN* 1.3 55.7 + - - +
43E GLN* 3.2 6.6 + - - +
44E LEU* 2.8 47.5 + - + +
125E LEU* 3.6 22.2 - - + -
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP 2.8 23.3 + - - +
38E GLU* 3.5 19.5 + - - +
40E VAL* 1.3 73.6 - - - +
42E LYS* 1.3 63.4 + - + +
44E LEU* 3.3 4.0 + - - +
45E ASP 3.1 11.3 + - - -
124E ALA 2.9 25.7 + - - -
125E LEU* 3.5 9.2 - - - +
126E ILE* 2.7 43.1 + - + +
129E ASN* 2.8 31.0 + - - +
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Residues in contact with LYS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLU* 3.0 30.6 + - + +
39E ASP* 3.8 17.1 + - - +
41E ASN* 1.3 79.9 - - + +
43E GLN* 1.3 58.4 + - - +
45E ASP* 3.2 9.2 + - - +
46E ARG* 2.9 50.3 + - - +
129E ASN* 4.9 0.2 - - - +
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Residues in contact with GLN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.3 20.9 - - + +
30E LEU* 3.8 23.3 - - + -
34E TYR* 3.5 26.4 + - + +
39E ASP 2.8 21.7 + - - +
40E VAL* 3.6 4.7 - - - +
42E LYS* 1.3 75.1 - - - +
44E LEU* 1.3 54.9 + - - +
46E ARG* 2.6 48.1 + - - +
47E MET* 2.9 44.8 + - - +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TYR* 3.5 27.1 - - + +
26E LEU* 4.4 9.6 - - + -
27E VAL* 4.3 12.8 - - + -
30E LEU* 3.6 21.3 - - + -
40E VAL* 2.8 38.0 + - + +
41E ASN* 3.6 5.2 - - - +
43E GLN* 1.3 72.7 - - - +
45E ASP* 1.3 58.3 + - - +
47E MET* 3.4 3.3 + - - -
48E GLY 2.8 24.4 + - - -
125E LEU* 5.0 0.7 - - + -
126E ILE 3.8 13.9 - - - +
127E TYR* 3.6 22.7 - - - +
129E ASN* 4.0 3.8 - - + -
130E LEU* 3.5 25.9 - - + +
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Residues in contact with ASP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ASN 3.1 12.6 + - - +
42E LYS* 3.5 11.3 - - - +
44E LEU* 1.3 77.4 - - - +
46E ARG* 1.3 59.7 + - - +
49E TYR* 2.9 24.4 + - - +
129E ASN* 3.8 20.6 + - - +
132E CYS* 3.9 9.2 - - - +
133E GLY* 3.2 18.3 + - - -
136E ARG* 2.6 45.4 + - - -
148E ALA 4.9 1.7 - - - +
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Residues in contact with ARG 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 4.4 7.9 + - - -
39E ASP* 4.7 2.0 + - - +
42E LYS* 2.9 31.5 + - - +
43E GLN* 2.6 49.0 - - - +
44E LEU 3.3 0.2 - - - -
45E ASP* 1.3 79.5 - - - +
47E MET* 1.3 62.3 + - + +
49E TYR* 3.0 20.3 + - + +
50E ASN* 3.1 21.1 + - - +
136E ARG* 5.0 2.0 - - - +
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Residues in contact with MET 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.6 41.6 - - + +
36B MET* 4.0 4.0 - - - +
39B TYR* 3.6 29.6 - - + -
26E LEU* 3.8 39.0 - - + -
30E LEU* 4.3 5.2 - - - -
43E GLN* 2.9 49.6 + - - +
44E LEU* 3.8 4.5 - - - +
46E ARG* 1.3 75.5 - - - +
48E GLY* 1.3 63.1 + - - +
50E ASN* 3.3 4.1 + - - +
51E ILE* 3.0 27.1 + - - +
130E LEU* 3.9 10.5 - - + -
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Residues in contact with GLY 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E LEU 2.8 14.5 + - - -
45E ASP 3.7 1.1 - - - -
46E ARG 3.2 0.2 - - - -
47E MET* 1.3 76.2 - - - +
49E TYR* 1.3 51.8 + - - +
51E ILE* 3.2 2.2 + - - -
52E GLY 2.8 30.7 + - - -
130E LEU* 3.4 34.0 - - - +
133E GLY 3.3 6.7 - - - -
134E VAL* 3.1 13.6 - - - +
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP 2.9 13.3 + - - +
46E ARG* 3.0 13.0 + - + +
48E GLY* 1.3 76.3 - - - +
50E ASN* 1.3 73.2 + - - +
52E GLY* 3.1 2.8 + - - -
53E VAL* 2.9 47.3 + - + +
133E GLY 3.3 11.4 - - - -
136E ARG* 3.9 27.1 - - - +
137E GLY* 3.6 27.9 - - - -
140E GLU* 2.9 38.1 + - + -
141E MET* 4.6 2.4 - - - +
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Residues in contact with ASN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.1 39.3 + - - +
38B GLN* 5.0 4.8 - - - +
46E ARG* 3.1 17.3 + - - +
47E MET* 3.3 4.3 + - - +
49E TYR* 1.3 88.1 - - - +
51E ILE* 1.3 66.2 + - - +
53E VAL* 3.6 6.9 + - - +
54E ARG* 3.5 26.5 + - - +
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Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 3.8 27.6 - - + +
32B LEU* 3.9 35.9 - - + -
35B GLU* 3.3 23.3 - - + -
47E MET 3.0 14.4 + - - +
48E GLY 3.5 5.8 - - - +
50E ASN* 1.3 73.4 - - - +
52E GLY* 1.3 56.5 + - - +
54E ARG* 3.0 7.9 + - - +
55E LEU* 2.6 41.6 + - + +
130E LEU* 4.1 21.3 - - + -
134E VAL* 4.2 7.2 - - + -
1068E PLM 4.1 18.2 - - + -
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Residues in contact with GLY 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E GLY 2.8 12.2 + - - -
49E TYR 3.1 4.4 + - - -
51E ILE* 1.3 77.5 - - - +
53E VAL* 1.3 61.4 + - - +
55E LEU* 4.2 1.8 - - - -
56E ILE* 3.2 20.4 + - - +
134E VAL* 3.5 32.8 - - - -
137E GLY 4.1 0.2 - - - -
138E ALA* 3.4 18.8 - - - +
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Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TYR* 2.9 51.0 + - + +
50E ASN* 3.8 10.1 - - - +
51E ILE 3.2 0.2 - - - -
52E GLY* 1.3 75.0 - - - +
54E ARG* 1.3 63.9 + - + +
56E ILE* 3.3 19.4 - - - +
57E GLU* 3.7 12.0 - - - +
137E GLY 3.9 7.6 - - - +
141E MET* 3.9 28.1 - - + +
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.9 22.5 - - + +
34B SER* 3.2 28.3 + - - -
35B GLU* 4.7 8.0 + - - -
38B GLN* 3.0 28.5 + - - +
50E ASN* 3.5 13.1 + - - +
51E ILE* 3.0 7.8 + - - +
53E VAL* 1.3 82.0 - - + +
55E LEU* 1.3 63.8 + - - +
56E ILE 3.4 0.2 - - - -
57E GLU* 3.6 19.2 + - - +
58E ASP* 3.7 10.9 + - - +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.0 16.6 - - + +
51E ILE* 2.6 22.9 + - + +
52E GLY* 3.3 4.2 + - - +
54E ARG* 1.3 70.2 - - - +
56E ILE* 1.3 71.2 + - - +
57E GLU 3.1 2.6 + - - -
58E ASP* 3.2 3.5 + - - +
59E PHE* 2.9 24.1 + - + -
86E TYR* 3.6 46.5 + - + +
134E VAL* 4.1 8.1 - - + -
138E ALA* 4.6 4.5 - - + -
1068E PLM 3.7 57.9 - - + -
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Residues in contact with ILE 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E GLY 3.2 11.0 + - - +
53E VAL 3.3 21.1 - - - +
55E LEU* 1.3 81.8 - - - +
57E GLU* 1.3 68.8 + - + +
59E PHE* 3.4 4.0 + - + +
60E LEU* 3.0 44.9 + - + +
138E ALA* 3.8 26.0 - - + +
141E MET* 3.7 21.3 - - + -
142E VAL* 4.1 21.8 - - + -
1068E PLM 3.9 28.5 - - + -
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 3.7 15.9 - - - +
54E ARG* 3.8 12.8 - - - +
55E LEU 3.1 0.4 - - - -
56E ILE* 1.3 85.4 - - + +
58E ASP* 1.3 63.0 + - - +
59E PHE 3.0 5.4 + - - -
60E LEU* 3.4 7.7 + - - +
61E ALA* 3.3 23.6 + - - +
141E MET* 5.9 1.0 - - - +
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Residues in contact with ASP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.2 31.9 + - - -
31B LEU* 4.7 6.4 - - + +
54E ARG 3.7 9.4 + - - +
55E LEU* 3.2 11.0 + - - +
57E GLU* 1.3 78.7 - - - +
59E PHE* 1.3 56.8 + - - +
61E ALA* 4.4 4.7 - - - +
62E ARG* 3.3 42.3 + - - +
86E TYR* 3.7 12.4 + - - +
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 2.9 18.5 + - + +
56E ILE* 3.5 7.0 - - + +
57E GLU 3.0 0.2 - - - -
58E ASP* 1.3 76.4 - - - +
60E LEU* 1.3 80.4 + - + +
61E ALA 3.2 1.8 - - - -
62E ARG 3.0 14.0 + - - -
63E SER* 3.3 20.7 + - - -
77E VAL* 3.4 26.0 - - + -
81E VAL* 3.5 27.1 - - + -
82E ALA* 3.8 16.2 - - + -
85E MET* 3.9 14.4 - - + -
86E TYR* 3.0 32.3 - + + +
1068E PLM 3.5 35.7 - - + -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ILE* 3.0 38.6 + - + +
57E GLU* 3.4 6.9 + - + +
59E PHE* 1.3 92.5 - - + +
61E ALA* 1.3 63.9 + - - +
63E SER* 3.0 26.4 + - - +
64E ASN 4.6 14.0 - - - -
68E CYS 6.2 0.2 - - - +
142E VAL* 5.1 6.5 - - + -
1068E PLM 4.4 17.5 - - + +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLU 3.3 13.8 + - - +
58E ASP* 4.5 5.2 - - - +
59E PHE 3.2 0.4 - - - -
60E LEU* 1.3 79.1 - - - +
62E ARG* 1.3 61.6 + - + +
63E SER 3.0 8.8 + - - +
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.0 27.5 + - - -
26B VAL* 5.8 1.6 - - - +
27B SER* 3.0 24.6 + - - +
127B TYR 5.6 1.8 + - - -
128B ILE* 6.1 2.0 - - - +
129B SER* 4.6 13.9 + - - +
12E LYS* 4.9 19.0 + - - +
58E ASP* 3.3 32.9 + - - +
59E PHE 3.0 6.2 + - - +
61E ALA* 1.3 76.2 - - + +
63E SER* 1.3 61.9 + - - +
85E MET* 3.5 32.4 - - + +
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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