Contacts of the helix formed by residues 48 - 83 (chain D) in PDB entry 3OMA
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 48 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.1 16.4 + - - -
47D ALA* 1.3 79.5 - - - +
49D PRO* 1.4 71.0 - - - +
50D VAL* 3.6 3.9 + - - +
51D ALA 3.1 10.2 + - - -
52D THR* 3.1 9.5 + - - -
224D PHE* 2.7 39.3 + - - -
240D PHE* 4.6 2.0 - - - -
241D ARG 3.3 21.8 - - - -
243D GLU* 3.4 7.8 + - - -
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Residues in contact with PRO 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D SER* 1.4 87.5 - - - +
50D VAL* 1.3 56.4 + - + +
52D THR* 3.4 8.5 + - - -
53D GLN* 3.0 33.5 + - + +
125D ASN* 5.6 3.8 - - - +
239D TRP* 4.5 13.9 - - + -
241D ARG* 3.3 49.1 - - + +
243D GLU* 3.7 21.7 - - + +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D SER* 3.2 7.5 + - - +
49D PRO* 1.3 75.0 - - - +
51D ALA* 1.3 66.1 + - - +
53D GLN* 3.1 11.0 + - - +
54D ILE* 3.0 21.9 + - + +
125D ASN* 4.1 11.9 - - - +
126D GLN* 3.7 35.7 - - + +
224D PHE 4.1 4.3 - - - +
225D GLY 3.8 20.2 - - - +
226D VAL* 5.4 3.1 - - + -
239D TRP* 3.6 44.0 - - + +
240D PHE* 6.0 1.6 - - - -
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Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.6 15.0 - - - +
48D SER* 3.1 14.0 + - - +
50D VAL* 1.3 76.6 - - - +
52D THR* 1.3 54.6 + - - +
54D ILE* 3.2 6.1 + - - +
55D HIS* 2.8 42.8 + - + -
222D PRO 4.4 3.6 - - - +
223D ALA 3.2 28.0 - - - +
224D PHE 3.8 7.6 + - - -
225D GLY* 3.9 10.1 - - - +
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 2.7 26.9 + - - -
48D SER 3.1 8.4 + - - -
49D PRO* 3.5 13.7 - - + +
51D ALA* 1.3 77.1 - - - +
53D GLN* 1.3 58.6 + - + +
55D HIS* 3.4 7.4 + - + +
56D TRP* 3.0 28.8 + - + +
243D GLU* 4.3 5.9 + - - -
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Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PRO* 3.0 18.0 + - + +
50D VAL* 3.1 14.5 + - - +
52D THR* 1.3 73.9 - - + +
54D ILE* 1.3 59.9 + - - +
56D TRP* 3.8 7.4 - - - +
57D LEU* 2.9 32.2 + - - +
121D PRO 5.7 0.6 - - - -
122D VAL* 3.9 37.8 - - + +
125D ASN* 2.7 40.9 + - - +
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C SER 3.4 21.5 - - - +
406C VAL* 4.5 12.2 - - + +
408C ARG* 4.8 1.3 - - + -
409C TYR* 4.3 28.3 - - + -
43D PHE* 4.4 17.3 - - + -
50D VAL* 3.0 15.6 + - + +
51D ALA* 3.5 7.6 - - - +
53D GLN* 1.3 72.4 - - - +
55D HIS* 1.3 62.1 - - + +
57D LEU* 3.3 4.5 + - - +
58D ASP* 2.8 30.5 + - - +
122D VAL* 5.2 3.1 - - + -
126D GLN* 3.4 23.3 - - - +
225D GLY* 3.7 33.9 - - - +
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Residues in contact with HIS 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TYR* 5.1 7.4 - + - -
43D PHE* 3.5 44.7 + + + +
44D GLN 3.1 22.8 + - - -
45D PRO* 4.6 1.0 - - + +
46D SER* 3.7 24.8 + - - -
51D ALA* 2.8 32.3 + - + -
52D THR* 3.4 10.8 - - + +
54D ILE* 1.3 78.1 - - + +
56D TRP* 1.3 63.0 + - - +
58D ASP* 3.6 2.1 + - - +
59D GLY* 3.0 20.1 + - - -
222D PRO 5.3 1.1 - - - -
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Residues in contact with TRP 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D THR* 3.0 18.7 + - + +
53D GLN* 3.8 7.6 - - - +
54D ILE 3.2 0.2 - - - -
55D HIS* 1.3 76.4 - - - +
57D LEU* 1.3 82.2 + - + +
59D GLY* 3.2 2.8 + - - -
60D PHE* 3.0 49.4 + + + +
118D PHE* 3.7 48.5 - + + -
122D VAL* 5.7 4.7 - - + -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C GLN* 5.1 0.2 - - + -
405C SER* 3.4 26.5 - - - +
406C VAL* 3.8 14.8 - - + -
53D GLN 2.9 18.8 + - - +
54D ILE* 3.9 2.5 - - - +
56D TRP* 1.3 85.9 - - + +
58D ASP* 1.3 57.3 + - - +
60D PHE* 3.3 10.9 + - + +
61D ILE* 3.0 50.2 + - + +
115D ILE 4.8 1.6 - - - +
118D PHE* 4.0 33.9 - - + +
119D SER* 3.9 22.0 - - - +
122D VAL* 4.3 11.4 - - + -
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C VAL* 3.9 9.5 - - - +
406C VAL* 3.8 14.1 - - + +
410C TYR* 2.7 35.0 + - - -
415C TYR* 5.0 1.2 + - - -
476C ARG* 2.6 28.0 + - - -
43D PHE* 3.3 19.6 - - + -
54D ILE 2.8 21.5 + - - +
55D HIS 3.9 0.2 - - - +
57D LEU* 1.3 72.7 - - - +
59D GLY* 1.3 54.9 + - - +
61D ILE* 3.5 5.4 + - - +
62D LEU* 2.8 36.7 + - - +
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Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ARG* 6.3 0.2 - - - -
55D HIS 3.0 15.4 + - - -
56D TRP* 3.2 4.4 + - - -
58D ASP* 1.3 75.1 + - - +
60D PHE* 1.3 63.5 + - - +
62D LEU* 3.4 9.5 + - - +
63D VAL* 3.2 30.4 + - - +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TRP* 3.0 40.1 + + + +
57D LEU* 3.5 18.8 - - + +
59D GLY* 1.3 74.1 - - - +
61D ILE* 1.3 68.0 + - + +
63D VAL* 3.5 7.8 + - + +
64D ILE* 3.1 44.8 + - + +
114D ALA* 4.9 8.1 - - + -
115D ILE* 4.3 23.6 - - + -
118D PHE* 3.6 40.4 - + + -
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ILE* 5.4 2.9 - - + -
400C VAL* 3.8 33.4 - - + +
403C GLN* 3.8 30.3 - - + -
406C VAL* 4.7 5.6 - - + -
57D LEU* 3.0 36.9 + - + +
58D ASP* 4.0 4.9 - - - +
60D PHE* 1.3 80.5 - - + +
62D LEU* 1.3 60.1 + - - +
64D ILE* 3.2 8.1 + - - +
65D ILE* 2.9 38.6 + - + +
115D ILE* 4.0 29.6 - - + -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C VAL* 5.7 0.8 - - - +
415C TYR* 5.9 0.7 - - - +
476C ARG* 4.3 13.7 - - - +
3D TRD 3.9 70.0 - - + -
58D ASP* 2.8 25.1 + - - +
59D GLY* 3.7 9.9 - - - +
60D PHE 3.3 0.2 - - - -
61D ILE* 1.3 74.2 - - - +
63D VAL* 1.3 58.2 + - + +
65D ILE* 3.5 11.5 - - + +
66D ALA* 2.8 39.4 + - + +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLY 3.2 16.0 + - - +
60D PHE* 3.7 11.0 - - + +
61D ILE 3.2 0.2 - - - -
62D LEU* 1.3 74.5 - - + +
64D ILE* 1.3 72.6 + - + +
66D ALA* 3.9 4.4 - - - +
67D ALA* 3.0 26.0 + - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 6.3 0.2 - - + -
60D PHE* 3.1 39.5 - - + +
61D ILE* 3.2 9.8 + - - +
63D VAL* 1.3 83.0 - - + +
65D ILE* 1.3 59.1 + - + +
67D ALA* 3.2 7.1 + - - +
68D ILE* 3.0 37.2 + - + +
111D ILE* 3.7 33.2 - - + -
115D ILE* 4.3 17.5 - - + -
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 5.2 6.7 - - + -
396C VAL* 3.7 42.7 - - + +
397C THR* 4.6 1.3 - - + +
399C ILE* 5.3 3.8 - - + -
400C VAL* 3.6 25.6 - - + -
415C TYR* 4.9 0.9 - - - +
3D TRD 4.1 23.3 - - + -
61D ILE* 2.9 35.4 + - + +
62D LEU* 3.5 14.6 - - + +
64D ILE* 1.3 75.7 - - + +
66D ALA* 1.3 64.1 + - - +
68D ILE* 3.8 10.2 - - + +
69D THR* 2.9 34.1 + - - -
115D ILE* 5.5 2.0 - - + -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TRD 4.5 8.3 - - + -
62D LEU* 2.8 27.7 + - + +
63D VAL* 3.9 4.9 - - - +
65D ILE* 1.3 76.4 - - - +
67D ALA* 1.3 52.6 + - - +
69D THR* 3.3 5.0 + - - -
70D ILE* 2.8 46.7 + - + +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D VAL* 3.0 22.3 + - + +
64D ILE* 3.4 7.4 - - - +
66D ALA* 1.3 73.4 - - - +
68D ILE* 1.3 56.2 + - + +
70D ILE* 3.3 6.8 + - - +
71D PHE* 2.8 36.1 + - - +
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.8 68.2 - - + -
364C PHE* 6.1 1.3 - - + -
392C THR* 5.0 1.1 - - + -
396C VAL* 4.4 10.1 - - + -
64D ILE* 3.0 37.4 + - + +
65D ILE* 3.8 9.4 - - + +
67D ALA* 1.3 74.5 - - + +
69D THR* 1.3 58.3 + - - +
71D PHE* 3.5 8.9 - - + +
72D VAL* 3.0 31.0 + - + +
111D ILE* 4.2 15.0 - - + -
----------------------------------------------------------
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PHE* 4.3 6.1 - - + -
392C THR* 4.0 18.1 + - + +
393C VAL* 4.0 24.5 - - + -
396C VAL* 3.8 19.6 - - - +
3D TRD 4.0 9.7 - - + +
65D ILE 2.9 23.5 + - - -
66D ALA* 3.7 6.3 - - - -
68D ILE* 1.3 74.1 - - - +
70D ILE* 1.3 65.7 + - + +
72D VAL* 4.0 1.0 - - - +
73D THR* 2.6 42.8 + - - +
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ALA* 2.8 35.5 + - + +
67D ALA* 3.7 6.1 - - - +
69D THR* 1.3 75.4 - - + +
71D PHE* 1.3 58.2 + - - +
73D THR* 3.2 6.5 + - - +
74D LEU* 2.8 58.8 + - + +
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C PHE* 4.7 15.0 - + - -
67D ALA 2.8 18.4 + - - +
68D ILE* 3.5 11.2 - - + +
70D ILE* 1.3 77.7 - - - +
72D VAL* 1.3 63.1 + - + +
74D LEU* 3.3 4.6 + - - +
75D LEU* 3.0 63.9 + - + +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 4.2 24.2 - - + -
363C ILE* 4.3 8.1 - - + -
364C PHE* 4.3 17.5 - - + -
367C ILE* 4.1 11.6 - - + +
388C LEU 4.6 2.7 - - - +
389C PHE* 5.3 2.0 - - + -
392C THR* 4.0 23.8 - - + +
68D ILE* 3.0 19.0 + - + +
69D THR 4.1 3.4 - - - +
71D PHE* 1.3 80.9 - - + +
73D THR* 1.3 64.3 + - - +
75D LEU* 3.4 7.9 + - + +
76D ILE* 3.1 41.9 + - + +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PHE* 3.0 41.7 - - + -
69D THR* 2.6 24.0 + - - +
70D ILE* 3.6 7.4 - - - +
72D VAL* 1.3 79.1 - - - +
74D LEU* 1.3 61.1 + - + +
76D ILE* 3.5 8.7 + - - +
77D LEU* 3.1 45.0 + - + +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 2.8 42.6 + - + +
71D PHE* 4.0 3.4 - - - +
73D THR* 1.3 74.2 - - + +
75D LEU* 1.3 59.9 + - - +
77D LEU* 4.0 17.6 - - + +
78D TYR* 2.8 32.4 + - - +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C PHE* 5.3 6.5 - - + -
367C ILE* 4.3 29.6 - - + -
371C TRP* 3.8 30.3 - - + -
71D PHE* 3.0 58.7 + - + +
72D VAL* 3.6 5.8 - - - +
74D LEU* 1.3 76.9 - - - +
76D ILE* 1.3 57.0 + - - +
78D TYR* 3.8 4.2 - - + +
79D ALA* 2.9 31.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE* 4.1 9.2 - - + -
370C MET* 4.0 20.6 - - + +
385C LEU* 4.2 32.1 - - + +
388C LEU* 3.7 30.3 - - + -
389C PHE* 4.3 12.6 - - + +
72D VAL* 3.1 33.4 + - + +
73D THR* 3.8 8.3 - - - +
74D LEU 3.3 0.2 - - - -
75D LEU* 1.3 76.0 - - - +
77D LEU* 1.3 64.7 + - + +
79D ALA* 3.9 1.2 - - - +
80D VAL* 3.0 33.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 3.1 37.5 + - + +
74D LEU* 4.0 18.4 - - + +
76D ILE* 1.3 78.5 - - + +
78D TYR* 1.3 65.2 + - - +
80D VAL* 3.6 8.4 + - + +
81D TRP* 3.1 23.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C TRP* 3.5 39.7 - + - -
74D LEU 2.8 19.5 + - - +
75D LEU* 3.8 4.5 - - + +
77D LEU* 1.3 77.8 - - - +
79D ALA* 1.3 55.1 + - - +
81D TRP* 3.0 24.2 + + - +
82D ARG* 2.7 71.5 + - + +
83D PHE* 4.8 0.7 - + - -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE* 5.4 0.2 - - + -
370C MET* 4.4 28.5 - - + +
371C TRP* 4.3 14.1 - - + -
375C ILE* 3.6 4.0 - - + +
75D LEU 2.9 19.0 + - - +
76D ILE 3.9 3.8 - - - +
78D TYR* 1.3 76.8 - - - +
80D VAL* 1.3 58.8 + - - +
83D PHE* 2.8 53.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET* 4.9 1.6 - - - -
375C ILE* 4.1 16.9 - - + +
377C LEU* 3.9 34.3 - - + -
385C LEU* 3.7 30.7 - - + -
76D ILE* 3.0 27.0 + - + +
77D LEU* 4.0 9.6 - - + +
79D ALA* 1.3 75.3 - - - +
81D TRP* 1.3 57.7 + - - +
84D HIS* 3.2 28.8 + - + +
----------------------------------------------------------
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Residues in contact with TRP 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU 3.1 17.9 + - - +
78D TYR* 3.0 25.4 + + - +
80D VAL* 1.3 81.4 - - - +
82D ARG* 1.3 91.7 + - + +
83D PHE 3.6 0.3 + - - -
84D HIS* 3.8 7.0 + - - +
87D ARG* 3.3 60.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 2.7 50.1 + - + +
81D TRP* 1.3 92.0 - - + +
83D PHE* 1.3 93.5 + - + +
84D HIS 3.5 0.2 - - - -
87D ARG* 3.2 33.1 + - - +
88D ASN* 4.3 15.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET 4.2 4.3 - - - -
371C TRP* 3.8 39.7 - + - -
372C GLY* 3.5 37.9 - - - -
373C GLY 3.3 19.9 - - - +
374C SER* 3.5 0.2 - - - -
375C ILE* 2.7 38.8 + - + +
78D TYR* 4.8 1.1 - + - -
79D ALA* 2.8 33.8 + - - +
82D ARG* 1.3 107.8 - - + +
84D HIS* 1.3 57.3 + - - +
88D ASN* 3.9 19.7 - - - -
----------------------------------------------------------
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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