Contacts of the helix formed by residues 28 - 59 (chain H) in PDB entry 2FJC
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 ASP 28 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO* 1.3 72.8 - - - +
29H ALA* 1.3 61.3 + - - +
30H ARG* 2.6 41.2 + - - +
31H ALA* 2.6 25.6 + - - +
32H ILE* 2.9 25.6 + - - +
148H SER* 5.1 1.5 - - - -
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ASP* 1.3 72.8 + - - +
30H ARG* 1.3 65.2 + - - +
32H ILE* 3.2 14.6 + - - +
33H ALA* 3.0 20.5 + - - +
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ASP* 2.6 16.5 + - - +
29H ALA* 1.3 73.4 - - - +
31H ALA* 1.3 68.7 + - - +
33H ALA* 2.7 31.3 + - + +
34H ALA* 2.9 27.6 + - - +
144H LEU* 5.6 6.9 - - - +
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Residues in contact with ALA 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO* 4.8 0.7 - - + -
28H ASP* 2.6 30.6 + - - +
30H ARG* 1.3 85.5 - - - +
32H ILE* 1.3 55.9 + - - +
34H ALA* 3.2 5.4 + - - +
35H ILE* 2.9 37.2 + - + +
144H LEU* 5.6 3.5 - - + +
148H SER* 3.5 32.5 - - - +
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Residues in contact with ILE 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO* 3.5 33.7 - - + +
28H ASP 2.9 24.4 + - - +
29H ALA* 3.2 12.3 - - - +
31H ALA* 1.3 75.6 - - - +
33H ALA* 1.3 58.0 + - - +
35H ILE* 3.4 8.5 + - + +
36H CYS* 2.9 42.8 + - - -
93H LEU* 4.3 29.2 - - + +
150H ASP* 6.0 0.2 - - - +
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Residues in contact with ALA 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ALA 3.0 10.4 + - - +
30H ARG* 2.7 22.0 + - + +
32H ILE* 1.3 71.1 - - - +
34H ALA* 1.3 63.0 + - - +
36H CYS* 3.3 7.1 + - - +
37H GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ARG* 2.9 28.3 + - - +
31H ALA* 3.6 10.3 - - - +
33H ALA* 1.3 75.6 - - - +
35H ILE* 1.3 63.0 + - - +
37H GLU* 3.3 8.9 + - - +
38H GLN* 3.1 25.1 + - - +
144H LEU* 4.3 20.0 - - + -
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Residues in contact with ILE 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO* 5.3 1.6 - - + -
31H ALA* 2.9 22.6 + - + +
32H ILE* 3.7 7.9 - - - +
34H ALA* 1.3 76.8 - - - +
36H CYS* 1.3 57.6 + - - +
38H GLN* 3.0 9.8 + - - +
39H LEU* 2.8 46.9 + - + +
93H LEU* 4.1 9.9 - - + -
141H THR* 4.6 4.7 - - + +
144H LEU* 4.1 20.4 - - + -
145H ALA* 3.8 16.4 - - + +
148H SER* 3.5 24.9 - - - +
150H ASP* 3.8 16.8 - - + +
153H THR* 4.0 17.3 - - + -
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Residues in contact with CYS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ILE* 2.9 30.6 + - - +
33H ALA* 3.7 7.0 - - - +
35H ILE* 1.3 76.4 - - - +
37H GLU* 1.3 58.9 + - - +
39H LEU* 4.2 1.6 - - - -
40H ARG* 2.8 34.9 + - - +
90H LEU* 3.5 24.4 - - + +
93H LEU* 3.8 33.7 - - - -
95H ALA* 4.1 14.6 - - + -
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Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ALA 3.0 14.3 + - - +
34H ALA* 3.5 12.6 - - - +
35H ILE 3.2 0.4 - - - -
36H CYS* 1.3 77.2 - - - +
38H GLN* 1.3 64.7 + - + +
40H ARG* 3.2 41.0 + - - +
41H GLN* 3.2 20.6 + - - +
107H LEU* 5.1 1.6 - - - +
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Residues in contact with GLN 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ALA 3.1 14.7 + - - +
35H ILE 3.0 8.8 + - - +
37H GLU* 1.3 76.7 + - - +
39H LEU* 1.3 65.0 + - - +
41H GLN* 3.0 9.6 + - - +
42H HIS* 2.9 30.6 + - - -
137H ARG* 3.2 38.9 + - - +
140H GLN* 3.6 17.3 + - - +
141H THR* 3.1 33.1 + - + +
144H LEU* 4.2 18.2 - - + -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ILE* 2.8 25.5 + - + +
36H CYS* 3.6 4.9 - - - +
38H GLN* 1.3 77.2 - - - +
40H ARG* 1.3 62.7 + - - +
42H HIS* 3.0 14.7 + - + +
43H VAL* 3.0 27.0 + - - +
86H ILE* 3.8 17.9 - - + +
89H ARG* 4.2 12.6 - - + -
90H LEU* 3.6 28.5 - - + -
93H LEU* 3.7 29.6 - - + -
141H THR* 3.7 24.2 - - + -
153H THR* 4.2 1.6 - - + -
157H ILE* 4.2 14.1 - - + -
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Residues in contact with ARG 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H CYS* 2.8 20.7 + - - +
37H GLU* 3.2 34.6 + - - +
39H LEU* 1.3 76.4 - - - +
41H GLN* 1.3 62.8 + - - +
43H VAL* 3.5 4.0 + - - +
44H ALA* 3.2 19.2 + - - +
90H LEU* 3.9 16.1 - - + +
96H GLN 4.6 8.3 + - - +
98H PRO* 3.6 34.4 - - + +
103H GLU* 4.9 5.3 + - - -
107H LEU* 3.1 46.4 - - + +
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU 3.2 8.5 + - - +
38H GLN* 3.0 13.1 + - - +
40H ARG* 1.3 77.8 - - - +
42H HIS* 1.3 63.2 + - - +
44H ALA* 3.1 6.6 + - - +
45H ASP* 2.8 42.3 + - - +
107H LEU* 3.8 30.0 + - + +
109H GLY* 5.0 3.0 - - - +
133H TYR* 4.1 8.0 + - - -
137H ARG* 2.7 45.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H GLN* 2.9 32.7 + - - -
39H LEU* 3.0 21.3 + - + +
41H GLN* 1.3 81.2 + - - +
43H VAL* 1.3 57.1 + - - +
45H ASP* 3.2 7.9 + - - +
46H LEU* 2.8 37.9 + - - +
86H ILE* 3.9 11.7 - - + -
134H LEU* 5.4 2.0 - - - +
137H ARG* 3.7 28.7 - - + +
138H PHE* 3.3 41.1 - + + -
141H THR* 2.6 32.2 + - - -
157H ILE* 5.0 1.1 - - + -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.5 6.3 - - + -
39H LEU 3.0 19.5 + - - +
40H ARG 3.7 7.2 - - - +
42H HIS* 1.3 76.4 - - - +
44H ALA* 1.3 58.4 + - - +
46H LEU* 3.4 3.3 + - - -
47H GLY* 2.8 26.0 + - - -
83H PHE* 3.4 32.9 - - + +
86H ILE* 3.8 17.9 - - + -
87H ALA* 3.8 22.2 - - + +
90H LEU* 4.5 8.3 - - + -
98H PRO* 3.8 11.9 - - + +
104H TYR* 3.7 19.6 - - + +
----------------------------------------------------------
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Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG 3.2 7.1 + - - +
41H GLN 3.1 9.1 + - - +
43H VAL* 1.3 79.5 - - - +
45H ASP* 1.3 62.2 + - - +
47H GLY* 3.3 1.6 + - - -
48H VAL* 3.0 27.7 + - - +
104H TYR* 3.5 27.6 - - + +
107H LEU* 3.6 31.6 - - + -
108H SER* 3.8 11.7 - - - +
----------------------------------------------------------
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Residues in contact with ASP 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H GLN* 2.8 34.9 + - - +
42H HIS* 3.8 4.6 + - - +
44H ALA* 1.3 71.9 - - - +
46H LEU* 1.3 58.6 + - - +
48H VAL* 3.2 2.9 + - - +
49H LEU* 2.8 30.1 + - - +
108H SER* 2.7 18.9 + - - -
109H GLY 2.7 29.7 + - - -
110H ILE* 3.6 16.5 + - + +
133H TYR* 3.3 28.9 + - - -
134H LEU* 3.7 15.2 - - + +
137H ARG* 4.8 1.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H HIS 2.8 26.3 + - - +
43H VAL* 3.7 4.9 - - - +
45H ASP* 1.3 71.6 - - - +
47H GLY* 1.3 57.5 + - - +
49H LEU* 3.2 1.4 + - - -
50H TYR* 2.8 31.8 + - - +
79H VAL* 3.4 33.0 - - + +
82H ALA* 4.0 7.6 - - + +
83H PHE* 3.9 31.0 - - + +
86H ILE* 3.9 15.3 - - + -
134H LEU* 3.5 31.0 - - + -
138H PHE* 3.9 25.1 - - + -
160H ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ILE* 5.5 1.5 - - - +
101E MET* 3.3 20.9 - - - +
43H VAL 2.8 18.0 + - - -
44H ALA 3.7 2.0 - - - -
46H LEU* 1.3 78.7 - - - +
48H VAL* 1.3 60.5 + - - +
50H TYR* 3.3 18.8 - - - +
51H ILE* 3.5 6.1 + - - +
83H PHE* 3.6 17.4 - - - -
104H TYR* 4.6 3.4 - - - -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E MET* 3.8 23.3 - - - -
44H ALA 3.0 18.5 + - - +
45H ASP 3.6 6.5 - - - +
47H GLY* 1.3 72.1 - - - +
49H LEU* 1.3 66.4 + - - +
51H ILE* 3.3 4.5 + - - +
52H LYS* 3.0 21.4 + - + +
104H TYR* 4.3 6.5 - - + +
105H LEU* 4.6 7.4 - - + -
108H SER* 3.4 22.9 - - - +
110H ILE* 3.6 32.3 - - + +
112H GLU* 4.0 24.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ASP 2.8 19.9 + - - +
46H LEU* 3.6 5.8 - - - +
48H VAL* 1.3 71.9 - - - +
50H TYR* 1.3 57.7 + - - +
52H LYS* 4.0 12.6 - - + -
53H LEU* 2.7 57.6 + - + +
56H TYR* 6.0 0.7 - - + -
79H VAL* 3.9 13.5 - - + -
110H ILE* 4.2 13.7 - - + +
127H VAL* 5.6 2.7 - - + -
130H ASP* 4.3 20.0 - - + +
131H PHE* 3.7 24.9 - - + -
134H LEU* 3.5 30.5 - - + -
----------------------------------------------------------
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Residues in contact with TYR 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 3.4 37.2 + + - -
51E ILE* 6.5 0.9 - - + -
80E THR* 2.7 29.8 + - - +
83E PHE* 5.3 4.7 - + - -
46H LEU 2.8 13.4 + - - +
47H GLY* 3.3 13.7 - - - +
48H VAL 3.2 0.4 - - - -
49H LEU* 1.3 79.0 - - - +
51H ILE* 1.3 72.2 + - + +
53H LEU* 3.6 4.0 + - - +
54H HIS* 2.8 53.9 + + - -
76H TYR* 3.3 40.8 - + + -
79H VAL* 4.0 8.9 - - + +
80H THR* 3.6 21.8 - - + +
83H PHE* 6.2 1.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLY* 5.6 1.6 - - - -
50E TYR* 6.6 0.4 - - + -
51E ILE* 5.0 2.9 - - + -
83E PHE* 5.0 7.6 - - + -
99E ALA* 3.7 5.6 - - - +
100E SER* 3.6 33.7 - - - +
101E MET* 3.6 32.5 - - + +
104E TYR* 3.5 31.9 - - + +
47H GLY 3.5 3.7 + - - +
48H VAL 3.3 6.5 + - - +
49H LEU 3.2 0.2 - - - -
50H TYR* 1.3 89.8 - - + +
52H LYS* 1.3 67.2 + - - +
54H HIS* 3.0 10.1 + - + +
55H ASN* 3.0 19.1 + - - +
101H MET* 3.8 11.7 - - + -
112H GLU* 4.8 1.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ALA 4.9 3.1 - - - -
48H VAL* 3.0 16.9 + - + +
49H LEU* 3.4 11.0 - - + +
51H ILE* 1.3 79.5 - - - +
53H LEU* 1.3 62.8 + - - +
55H ASN* 3.0 24.1 + - - +
56H TYR* 3.2 41.6 + - + -
110H ILE* 3.8 10.1 - - + +
111H ALA* 2.7 34.4 + - - +
112H GLU* 4.4 2.0 - - - -
113H GLU* 4.0 24.2 - - + +
126H ARG* 5.3 3.0 + - - +
130H ASP* 2.7 37.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 2.7 40.7 + - + +
50H TYR 3.8 4.0 - - - +
52H LYS* 1.3 74.5 - - - +
54H HIS* 1.3 56.6 + - - +
56H TYR* 3.4 7.3 + - + +
57H HIS* 2.8 29.1 + - - +
72H LEU* 4.1 14.2 - - + +
75H TYR* 3.9 15.0 - - + -
76H TYR* 3.7 36.6 - - + +
79H VAL* 3.7 26.2 - - + -
127H VAL* 3.9 31.0 - - + -
131H PHE* 4.8 3.1 - - + -
----------------------------------------------------------
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Residues in contact with HIS 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E THR* 4.7 1.6 + - - -
83E PHE* 3.5 27.4 - + + -
84E ASP* 3.5 23.9 + - - +
50H TYR* 2.8 58.5 + + - -
51H ILE* 3.0 12.7 + - + +
53H LEU* 1.3 75.6 - - - +
55H ASN* 1.3 56.5 + - - +
57H HIS* 3.0 7.0 + - - +
58H TRP* 2.8 58.8 + + + -
76H TYR* 3.3 37.0 + + - -
----------------------------------------------------------
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Residues in contact with ASN 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ALA* 3.1 36.0 + - + +
51H ILE 3.0 8.3 + - - +
52H LYS* 3.0 14.3 + - - +
54H HIS* 1.3 77.9 - - - +
56H TYR* 1.3 59.5 + - + +
58H TRP* 3.2 1.2 + - - -
59H HIS* 2.7 56.6 + - - +
113H GLU* 3.0 45.4 + - + +
115H GLU 3.5 14.3 + - - +
116H LYS* 4.8 4.2 - - - +
118H ILE* 5.6 0.7 - - - +
----------------------------------------------------------
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 6.0 0.4 - - + -
52H LYS* 3.2 49.0 + - + -
53H LEU* 3.8 8.1 - - + +
55H ASN* 1.3 77.7 - - - +
57H HIS* 1.3 65.2 + - - +
59H HIS 4.4 0.4 - - - +
60H ILE* 3.0 34.7 + - - +
72H LEU* 4.0 12.8 - - + -
113H GLU* 2.7 42.6 + - + -
118H ILE* 3.8 23.3 - - + -
123H ALA* 3.8 25.6 - - + -
126H ARG* 3.4 20.3 - - + +
127H VAL* 3.6 32.3 - - + -
130H ASP* 5.4 0.4 - - - -
----------------------------------------------------------
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Residues in contact with HIS 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ASP* 3.7 4.9 - - - -
605E FE 2.1 31.2 - - - -
53H LEU 2.8 18.5 + - - +
54H HIS* 3.1 11.2 - - - +
56H TYR* 1.3 77.7 - - - +
58H TRP* 1.3 83.4 + + - +
60H ILE* 4.3 6.1 - - - +
65H PHE* 4.3 1.2 - - - -
69H HIS* 2.7 78.1 + + - -
72H LEU* 3.9 14.5 - - + +
73H GLU* 3.9 24.7 + - + -
76H TYR* 3.8 12.3 + + + -
----------------------------------------------------------
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Residues in contact with TRP 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E VAL* 4.5 0.9 - - + -
83E PHE* 3.6 33.0 - + - -
84E ASP* 3.0 22.5 + - - -
87E ALA* 3.3 27.4 - - + +
88E GLU* 4.0 11.2 + - + +
91E LEU* 3.4 38.3 - - + +
97E ALA* 3.9 13.9 - - + -
98E PRO 3.5 20.9 - - - -
99E ALA* 3.7 16.4 - - + -
104E TYR* 3.7 4.7 - - - -
54H HIS* 2.8 49.2 + + + +
55H ASN* 3.8 2.0 - - - +
57H HIS* 1.3 90.6 - + - +
59H HIS* 1.3 72.0 + + - +
60H ILE 3.7 4.1 - - - +
65H PHE* 4.8 0.7 - - - -
69H HIS* 5.0 0.7 - + - -
169L TRP* 4.0 10.4 + - - -
----------------------------------------------------------
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Residues in contact with HIS 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 3.8 20.3 - - + +
96E GLN* 3.8 17.0 - - + +
97E ALA* 3.2 37.2 + - - -
99E ALA* 4.1 7.9 - - + -
55H ASN* 2.7 42.7 + - - +
58H TRP* 1.3 79.6 - + + +
60H ILE* 1.3 66.1 + - - +
61H TYR* 3.7 3.1 + - - +
116H LYS* 3.3 22.2 - - + +
117H GLU* 3.1 26.0 - - - +
118H ILE* 3.0 23.0 + - + +
176L LYS* 5.5 0.5 + - - -
----------------------------------------------------------
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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