Contacts of the helix formed by residues 42 - 69 (chain E) in PDB entry 1W88
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 42 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLU 4.3 0.4 + - - -
41E LEU* 1.3 74.2 - - - +
43E ASP* 1.3 57.4 + - - +
44E GLU* 3.8 8.5 + - - +
45E GLN* 2.8 49.1 + - - +
46E LEU* 3.0 10.6 + - - +
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Residues in contact with ASP 43 (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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41E LEU 3.7 1.1 + - - +
42E SER* 1.3 71.8 - - - +
44E GLU* 1.3 61.4 + - - +
46E LEU* 3.4 17.7 + - - +
47E LYS* 3.2 22.2 + - - +
306E LYS* 3.9 13.2 + - - -
308E LEU* 3.2 46.4 - - + +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E SER* 3.1 8.2 - - - +
43E ASP* 1.3 79.0 - - - +
45E GLN* 1.3 69.9 + - - +
47E LYS* 3.4 4.5 + - - +
48E GLU* 3.0 22.3 + - - +
51E ARG* 3.0 35.2 + - - -
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Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 4.0 23.5 - - + +
42E SER* 2.8 27.3 + - - +
44E GLU* 1.3 90.5 - - - +
46E LEU* 1.3 63.8 + - - +
47E LYS 3.2 1.8 - - - -
48E GLU* 4.2 10.6 - - - +
49E LEU* 3.1 17.3 + - - +
90E PHE* 3.2 36.6 - - + -
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E MET* 5.0 4.7 - - + -
41E LEU* 3.4 38.4 - - + +
42E SER 3.0 11.2 + - - +
43E ASP* 3.4 27.8 + - - +
45E GLN* 1.3 76.9 - - - +
47E LYS* 1.3 60.4 + - - +
49E LEU* 3.7 4.2 - - - +
50E MET* 3.3 15.6 + - - +
239E LEU* 4.2 19.5 - - + -
299E PHE* 3.5 23.7 - - + -
302E PHE* 4.0 25.4 - - + -
303E LEU* 4.3 8.5 - - + +
306E LYS* 4.8 11.7 - - - +
308E LEU* 4.4 10.3 - - + -
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Residues in contact with LYS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ASP 3.2 12.1 + - - +
44E GLU* 3.6 10.3 - - - +
45E GLN 3.2 0.2 - - - -
46E LEU* 1.3 76.0 - - - +
48E GLU* 1.3 54.5 + - - +
49E LEU 3.1 1.1 - - - -
50E MET* 2.9 8.6 + - - +
51E ARG* 2.8 57.2 + - - +
303E LEU* 5.8 2.5 - - - -
308E LEU* 4.6 17.0 - - + +
309E TRP* 4.0 7.1 - - + -
313E GLU* 5.1 2.2 - - - +
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 3.0 17.9 + - - +
45E GLN* 4.0 15.0 - - - +
47E LYS* 1.3 75.8 - - - +
49E LEU* 1.3 56.9 + - - +
51E ARG* 3.1 36.0 + - - +
52E ARG* 3.0 72.3 + - - +
90E PHE* 4.1 12.3 - - + -
110E TRP* 5.1 3.1 - - - -
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 4.9 12.1 - - + -
45E GLN 3.1 17.8 + - - +
46E LEU* 3.7 7.9 - - - +
47E LYS 3.1 0.4 - - - -
48E GLU* 1.3 77.4 - - - +
50E MET* 1.3 56.3 + - - +
52E ARG* 3.5 2.0 + - - +
53E MET* 3.0 42.6 + - + +
86E ILE* 3.9 27.4 - - + +
87E ALA* 4.1 9.0 - - + +
90E PHE* 3.8 34.2 - - + -
238E PRO* 4.2 23.8 - - + +
239E LEU* 5.3 0.7 - - + -
242E TYR* 5.4 2.0 - - + -
299E PHE* 4.0 21.8 - - + -
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Residues in contact with MET 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU 3.3 11.4 + - - +
47E LYS* 2.9 9.0 + - - +
49E LEU* 1.3 76.2 - - - +
51E ARG* 1.3 66.3 + - - +
53E MET* 3.1 3.8 + - - +
54E VAL* 2.8 32.7 + - + +
296E LEU* 3.5 33.7 - - + +
299E PHE* 3.6 29.4 - - + +
300E ARG* 3.4 38.1 - - + +
303E LEU* 4.6 3.6 - - + -
309E TRP* 3.4 47.1 - - + +
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Residues in contact with ARG 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLU* 3.0 33.6 + - - -
47E LYS* 2.8 36.1 + - - +
48E GLU* 3.1 32.5 + - - +
50E MET* 1.3 72.4 - - - +
52E ARG* 1.3 57.1 + - - +
54E VAL 3.2 0.2 + - - -
55E TYR* 2.8 28.7 + - - +
110E TRP* 5.4 0.4 - - - -
309E TRP* 3.9 14.3 - - + -
313E GLU* 4.5 13.9 + - + +
317E VAL* 3.4 38.6 - - + +
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Residues in contact with ARG 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E GLU* 3.0 47.5 + - - +
49E LEU 3.7 2.5 - - - +
51E ARG* 1.3 75.4 - - - +
53E MET* 1.3 57.6 + - - +
55E TYR 3.3 1.0 + - - -
56E THR* 2.9 35.0 + - - -
86E ILE* 3.5 20.4 - - + -
89E HIS* 4.0 23.2 + - - -
90E PHE* 3.3 38.6 - - - +
110E TRP* 3.6 48.9 + - + +
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Residues in contact with MET 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 3.0 29.5 + - + +
50E MET* 3.1 10.5 + - - +
52E ARG* 1.3 74.8 - - - +
54E VAL* 1.3 61.7 + - - +
56E THR 3.9 0.2 - - - -
57E ARG* 3.2 19.2 + - - +
82E GLU* 3.6 49.1 - - + +
83E ALA* 4.2 2.0 - - - -
86E ILE* 4.1 11.0 - - + -
87E ALA 5.3 0.7 - - - -
238E PRO* 3.6 30.3 - - + -
295E PRO* 4.6 5.6 - - - +
296E LEU* 4.2 16.1 - - + +
299E PHE* 3.2 42.8 - - + -
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Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E MET* 2.8 20.2 + - + +
51E ARG* 3.5 3.8 - - - +
53E MET* 1.3 74.3 - - - +
55E TYR* 1.3 65.5 + - - +
57E ARG* 3.1 17.0 + - - +
58E ILE* 3.1 14.1 + - + +
296E LEU* 3.7 24.2 - - + -
309E TRP* 4.0 17.0 - - + -
314E GLU* 4.0 18.8 - - + +
317E VAL* 3.7 24.5 - - + -
318E ILE* 3.8 25.8 - - + +
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Residues in contact with TYR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ARG 2.8 16.0 + - - +
52E ARG 3.6 4.3 - - - +
54E VAL* 1.3 79.8 - - - +
56E THR* 1.3 60.1 + - - +
58E ILE* 3.5 3.6 + - - +
59E LEU* 2.9 35.6 + - + +
109E ILE* 6.0 5.4 - - + -
110E TRP* 3.8 28.3 - + + -
115E LEU* 3.9 21.0 - - + +
317E VAL* 4.1 7.6 - - + -
320E GLN* 4.0 17.3 - - - -
321E ALA* 3.6 36.0 - - + +
324E GLU* 2.6 44.5 + - - +
325E ILE* 5.1 2.2 - - + -
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Residues in contact with THR 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 ARG 2.9 11.5 + - - -
53E MET 3.9 4.9 - - - -
55E TYR* 1.3 75.0 - - - +
57E ARG* 1.3 64.4 + - - +
59E LEU* 3.3 14.0 + - + +
60E ASP* 3.1 22.6 + - + +
78E THR* 5.8 2.9 - - - +
82E GLU* 3.9 17.9 - - + +
85E GLN* 4.8 2.9 - - - +
86E ILE* 3.5 10.6 - - + +
106E PRO* 3.9 30.3 - - + -
110E TRP* 2.7 31.0 + - - -
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Residues in contact with ARG 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 MET 3.2 13.8 + - - +
54E VAL 3.1 10.8 + - - +
56E THR* 1.3 75.5 - - - +
58E ILE* 1.3 65.3 + - + +
60E ASP* 3.2 4.3 + - - +
61E GLN* 3.1 47.5 + - - +
79E ALA* 4.5 12.9 - - - +
80E GLY* 3.9 14.0 - - - +
82E GLU* 3.0 41.7 + - - +
294E ASP* 3.0 42.0 + - - -
296E LEU* 3.7 25.6 - - + +
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Residues in contact with ILE 58 (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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54E VAL* 3.1 15.7 + - + +
55E TYR 3.8 6.3 - - - +
57E ARG* 1.3 81.3 - - + +
59E LEU* 1.3 62.6 + - - +
61E GLN* 3.8 22.6 - - + +
62E ARG* 3.0 38.9 + - + +
318E ILE* 3.8 42.0 - - + +
321E ALA* 3.9 16.2 - - + -
322E LYS* 3.8 34.3 - - + -
325E ILE* 4.3 1.6 - - + -
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E TYR* 2.9 23.9 + - + +
56E THR* 3.3 21.5 + - + +
58E ILE* 1.3 78.0 - - - +
60E ASP* 1.3 52.0 + - - +
62E ARG* 3.9 1.4 - - - +
63E SER* 2.6 43.0 + - - +
75E TYR* 5.8 1.1 - - + +
106E PRO* 5.2 10.1 - - + -
109E ILE* 3.9 26.9 - - + -
110E TRP* 6.3 0.7 - - - +
115E LEU* 3.7 24.5 - - + -
119E PHE* 3.9 20.2 - - + -
325E ILE* 3.7 19.2 - - + +
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Residues in contact with ASP 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E THR* 3.1 13.4 + - + +
57E ARG* 3.2 10.4 + - - +
59E LEU* 1.3 74.3 - - - +
61E GLN* 1.3 63.1 + - - +
63E SER* 3.1 2.4 + - - -
64E ILE* 2.8 46.4 + - - +
75E TYR* 2.3 37.9 + - - +
77E PRO* 3.5 2.8 - - - +
78E THR* 3.0 19.3 + - - +
79E ALA* 3.1 38.1 - - - +
82E GLU* 5.1 1.1 - - - +
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Residues in contact with GLN 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ARG* 3.1 45.2 + - - +
58E ILE* 3.5 22.3 + - + +
60E ASP* 1.3 80.8 - - - +
62E ARG* 1.3 63.1 + - + +
64E ILE* 3.5 10.0 + - + +
65E SER* 3.2 26.8 + - - -
322E LYS* 6.1 0.5 - - - -
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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
----------------------------------------------------------
58E ILE* 3.0 33.5 + - + +
59E LEU 4.1 2.7 - - - +
61E GLN* 1.3 80.0 - - + +
63E SER* 1.3 57.0 + - - +
65E SER* 3.6 24.0 + - - -
66E LEU* 2.9 60.6 + - - +
69E GLN* 5.0 5.7 + - - +
119E PHE* 6.3 0.2 - - + -
322E LYS* 4.5 23.7 - - + +
325E ILE* 4.1 29.6 - - + +
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Residues in contact with SER 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E LEU* 2.6 38.4 + - - +
60E ASP 3.1 5.1 + - - -
62E ARG* 1.3 74.7 - - - +
64E ILE* 1.3 64.1 + - - +
66E LEU* 4.3 0.9 - - - -
67E ASN* 2.9 26.2 + - - +
72E LEU* 3.5 16.8 - - - +
75E TYR* 3.5 31.8 - - - -
119E PHE* 4.0 12.6 - - - -
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Residues in contact with ILE 64 (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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60E ASP* 2.8 38.4 + - - +
61E GLN* 3.7 10.5 - - + +
63E SER* 1.3 72.5 - - - +
65E SER* 1.3 59.5 + - - +
67E ASN* 3.0 17.0 + - - +
68E ARG* 2.8 43.6 + - + +
75E TYR* 4.0 16.8 - - + -
77E PRO* 5.0 11.9 - - + -
79E ALA* 5.7 2.2 - - + -
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLN 3.2 12.5 + - - -
62E ARG* 3.6 24.9 + - - -
64E ILE* 1.3 77.5 - - - +
66E LEU* 1.3 58.6 + - - +
68E ARG* 3.1 26.2 + - - +
69E GLN* 2.9 47.2 + - - +
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ARG* 2.9 54.9 + - - +
63E SER* 4.3 1.1 - - - -
65E SER* 1.3 76.2 - - - +
67E ASN* 1.3 55.2 + - - +
69E GLN* 3.4 9.0 + - - +
70E GLY 3.4 3.1 + - - -
71E ARG* 2.7 59.7 + - + +
72E LEU* 3.2 24.6 + - + -
119E PHE* 4.6 4.0 - - + -
325E ILE* 4.4 16.6 - - + -
329E ILE* 3.7 35.0 - - + -
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Residues in contact with ASN 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E SER 2.9 19.4 + - - +
64E ILE* 3.4 12.5 - - - +
66E LEU* 1.3 73.6 - - - +
68E ARG* 1.3 70.0 + - - +
70E GLY* 3.1 14.2 + - - -
72E LEU* 3.7 23.4 + - + +
73E GLY 3.9 12.2 + - - +
75E TYR* 4.2 19.6 - - + +
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ILE* 2.8 30.1 + - + +
65E SER* 3.5 34.5 + - - +
67E ASN* 1.3 78.2 - - - +
69E GLN* 1.3 66.1 + - - +
70E GLY 3.1 3.9 + - - -
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Residues in contact with GLN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ARG* 5.0 6.2 + - - +
65E SER* 2.9 40.8 + - - +
66E LEU* 3.6 13.7 - - - +
67E ASN 3.2 0.4 - - - -
68E ARG* 1.3 83.0 - - + +
70E GLY* 1.3 61.9 + - - +
71E ARG* 3.1 28.9 + - - +
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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