Contacts of the helix formed by residues 45 - 71 (chain X) in PDB entry 1MFR
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 HIS 45 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LYS* 5.1 4.5 + - - -
142Q LYS* 4.0 2.5 - - - -
146Q ASP* 3.0 34.1 + - + -
37X PHE 4.6 1.8 - - - -
38X ASP* 3.4 44.2 + - - -
43X ALA* 3.3 15.3 + - + -
44X LEU* 1.3 68.8 - - - +
46X ASN* 1.3 64.7 + - - +
48X ALA* 3.5 6.5 - - - +
49X GLU* 3.1 30.9 + - + +
167X ASP* 3.6 3.4 + - - +
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Residues in contact with ASN 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X HIS* 1.3 77.1 - - - +
47X VAL* 1.3 66.0 + - - +
49X GLU* 3.3 8.6 + - - +
50X PHE 3.0 17.7 + - - -
167X ASP* 2.9 45.6 + - - +
168X LYS* 4.4 10.9 - - - +
171X VAL* 3.2 28.1 - - + +
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Residues in contact with VAL 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X PHE* 3.9 21.1 - - + -
44X LEU* 3.5 18.6 - - + +
46X ASN* 1.3 75.5 - - - +
48X ALA* 1.3 62.1 + - - +
50X PHE* 3.2 8.7 + - - +
51X PHE* 3.2 45.7 + - + -
92X THR* 4.1 26.7 - - + +
96X MET* 4.6 4.5 - - + -
163X GLU 5.8 0.4 - - - +
166X PHE* 4.3 13.2 - - + -
167X ASP* 3.1 23.3 + - + +
171X VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34X TYR* 3.2 40.5 - - + +
37X PHE* 3.7 25.1 - - + +
38X ASP* 4.1 4.0 - - + +
44X LEU 3.0 13.6 + - - +
45X HIS* 3.5 14.6 - - - +
46X ASN 3.2 0.2 - - - -
47X VAL* 1.3 77.9 - - - +
49X GLU* 1.3 57.7 + - - +
51X PHE* 3.4 1.9 + - - -
52X LYS 3.0 21.0 + - - -
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Residues in contact with GLU 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LYS* 5.8 1.6 - - - -
34X TYR* 3.6 23.2 + - - -
45X HIS* 3.1 17.9 + - + +
46X ASN* 3.3 11.8 + - - +
48X ALA* 1.3 73.8 - - - +
50X PHE* 1.3 61.5 + - - +
52X LYS* 3.6 24.6 + - - +
53X GLU* 2.9 39.0 + - - +
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Residues in contact with PHE 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X TYR* 5.9 0.2 - + - -
46X ASN 3.0 13.6 + - - +
47X VAL* 3.3 10.5 - - - +
49X GLU* 1.3 76.3 - - - +
51X PHE* 1.3 93.6 + + - +
53X GLU* 3.5 8.4 + - + +
54X HIS* 3.2 55.3 + + - -
96X MET* 4.0 20.9 - - + -
143X ARG* 3.9 18.6 - - - -
144X ILE* 4.5 11.4 - - + -
147X PHE* 3.7 28.5 - + - -
171X VAL* 3.7 19.7 - - + +
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Residues in contact with PHE 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X TYR* 3.6 49.2 - + + +
33X MET* 3.8 30.5 - - + -
34X TYR 4.0 4.0 - - - +
37X PHE* 3.7 22.4 - + - -
47X VAL* 3.2 37.6 + - + -
48X ALA 3.9 5.6 - - - +
50X PHE* 1.3 98.5 - + - +
52X LYS* 1.3 59.0 + - - +
54X HIS* 3.2 5.1 + - + +
55X SER* 2.9 24.3 + - - -
95X ALA* 4.1 11.9 - - + -
96X MET* 3.7 24.5 - - + -
99X ALA* 4.2 8.3 - - + -
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Residues in contact with LYS 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLU* 3.7 24.1 + - - +
34X TYR* 3.7 38.5 + - + +
48X ALA 3.0 17.6 + - - +
49X GLU* 3.6 33.1 + - - +
50X PHE 3.3 0.2 - - - -
51X PHE* 1.3 78.0 - - - +
53X GLU* 1.3 62.9 + - + +
55X SER* 3.2 20.8 + - - +
56X HIS* 3.3 29.7 + - + +
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Residues in contact with GLU 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X GLU* 2.9 26.7 + - + +
50X PHE* 3.6 8.7 - - + +
51X PHE 3.2 0.2 - - - -
52X LYS* 1.3 78.3 - - + +
54X HIS* 1.3 63.0 + - + +
56X HIS* 3.3 10.7 + - - +
57X GLU* 3.1 35.9 + - - +
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Residues in contact with HIS 54 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X TYR* 3.9 23.3 - + + -
50X PHE* 3.2 41.4 + + - +
51X PHE* 3.4 10.8 - - + +
53X GLU* 1.3 83.2 - - + +
55X SER* 1.3 63.2 + - - +
57X GLU* 3.4 17.3 + - - +
58X GLU* 3.2 32.7 + - - +
103X GLU* 3.6 17.9 + - - -
140X ASP* 3.7 27.1 - - + -
143X ARG* 3.1 27.3 + - - -
144X ILE* 4.9 4.3 - - + -
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Residues in contact with SER 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLU* 4.4 4.5 + - - -
27X SER* 2.9 47.7 + - - +
30X TYR* 3.7 14.5 - - - +
31X SER* 3.8 14.7 + - - -
51X PHE 2.9 9.1 + - - -
52X LYS* 3.2 17.0 + - - +
54X HIS* 1.3 74.2 - - - +
56X HIS* 1.3 76.3 + - - +
58X GLU 3.4 1.0 + - - -
59X ARG* 3.1 12.4 + - - +
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Residues in contact with HIS 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ARG* 6.2 2.0 - - + -
63J GLU* 3.1 29.4 + - - -
52X LYS* 3.3 34.5 + - + +
53X GLU* 3.3 11.5 + - - +
54X HIS 3.2 0.4 - - - -
55X SER* 1.3 90.9 + - - +
57X GLU* 1.3 56.0 + - - +
59X ARG* 3.5 8.3 + - + +
60X GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 57 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X GLU* 3.1 20.3 + - - +
54X HIS* 3.6 26.0 + - - +
55X SER 3.2 0.2 - - - -
56X HIS* 1.3 75.4 - - - +
58X GLU* 1.3 63.3 + - + +
60X GLU* 3.2 7.0 + - + +
61X HIS* 2.9 47.4 + - + +
140X ASP* 4.1 18.0 - - - +
143X ARG* 5.8 1.9 + - - -
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Residues in contact with GLU 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X GLU* 2.7 30.8 - - - +
26X ALA* 4.2 9.0 - - + -
27X SER* 3.8 12.1 - - - -
30X TYR* 4.0 16.4 - - + -
54X HIS* 3.2 21.7 + - - +
55X SER 3.4 0.2 + - - -
57X GLU* 1.3 81.0 - - - +
59X ARG* 1.3 57.9 + - - +
61X HIS* 3.1 11.0 + - - +
62X ALA* 3.0 26.0 + - - +
103X GLU* 3.4 15.0 - - - +
106X VAL* 4.9 0.8 - - - +
176X MG 2.0 32.3 - - - -
177X MG 2.6 25.0 - - - -
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Residues in contact with ARG 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J HIS* 6.0 2.7 - - + +
59J ARG* 5.7 9.0 - - + -
24X LEU* 4.9 11.6 - - + +
27X SER* 3.6 13.4 + - - +
55X SER 3.1 18.0 + - - +
56X HIS* 3.6 9.9 - - + +
57X GLU 3.1 0.2 - - - -
58X GLU* 1.3 74.1 - - - +
60X GLU* 1.3 63.8 + - - +
62X ALA* 3.2 8.9 + - - +
63X GLU* 3.1 37.0 + - + +
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Residues in contact with GLU 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X HIS 3.1 15.5 + - - +
57X GLU* 3.2 11.0 + - - +
59X ARG* 1.3 76.3 - - - +
61X HIS* 1.3 60.1 + - + +
63X GLU* 3.5 12.6 + - - +
64X LYS* 3.1 32.9 + - - +
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Residues in contact with HIS 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X GLU* 3.4 15.7 + - - +
57X GLU* 2.9 30.7 + - + +
58X GLU* 3.1 18.6 + - - +
59X ARG 3.2 0.2 - - - -
60X GLU* 1.3 79.1 - - + +
62X ALA* 1.3 63.8 + - - +
64X LYS* 3.4 18.8 + - - +
65X PHE* 3.3 12.9 + - - -
132X GLU 4.6 6.7 + - - -
133X TYR* 3.0 39.8 + + + -
136X GLU* 5.1 14.6 - - + +
137X GLN* 5.1 0.9 - - - -
140X ASP* 5.6 0.4 - - - -
176X MG 2.7 24.2 - - - -
177X MG 4.3 10.8 - - - -
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Residues in contact with ALA 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X LEU* 3.7 16.0 - - + +
23X GLU* 3.8 10.5 - - + +
24X LEU* 3.7 34.3 - - + -
58X GLU 3.0 12.2 + - - +
59X ARG 3.2 9.2 + - - +
61X HIS* 1.3 76.2 - - - +
63X GLU* 1.3 63.9 + - + +
65X PHE* 3.3 9.4 + - - +
66X MET* 3.1 26.5 + - + +
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Residues in contact with GLU 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER* 5.0 4.3 + - - +
34J TYR* 5.2 9.2 + - + -
52J LYS* 3.7 20.7 + - - +
55J SER* 4.5 5.4 + - - -
56J HIS* 3.0 35.5 + - - -
24X LEU* 6.4 0.4 - - + -
59X ARG* 3.1 25.2 + - + +
60X GLU* 3.8 12.3 - - - +
61X HIS 3.3 0.2 - - - -
62X ALA* 1.3 75.9 - - + +
64X LYS* 1.3 64.4 + - - +
66X MET* 3.2 25.2 + - + +
67X LYS* 3.1 24.3 + - - +
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Residues in contact with LYS 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X GLU* 3.1 20.0 + - - +
61X HIS* 3.6 17.4 + - - +
62X ALA 3.3 0.2 - - - -
63X GLU* 1.3 76.1 - - - +
65X PHE* 1.3 57.4 + - - +
67X LYS* 3.5 7.1 + - - +
68X TYR* 2.9 27.4 + - - +
128X PHE* 3.7 10.0 - - + -
132X GLU* 2.9 53.2 + - + +
133X TYR* 3.2 21.1 - - + +
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Residues in contact with PHE 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16X VAL* 3.9 30.3 - - + +
19X MET* 3.4 33.7 - - + -
20X LEU* 4.2 18.8 - - + -
23X GLU* 4.1 14.8 - - + -
61X HIS 3.3 16.9 + - - -
62X ALA 3.3 8.6 + - - +
63X GLU 3.2 0.6 - - - -
64X LYS* 1.3 77.4 - - - +
66X MET* 1.3 63.9 + - - +
68X TYR* 3.5 3.6 - - + +
69X GLN* 3.0 24.8 + - - +
110X LEU* 4.0 10.8 - - + -
113X LEU* 4.5 8.1 - - + -
128X PHE* 3.5 25.8 - + - -
129X LEU* 4.0 12.6 - - + -
133X TYR* 3.4 30.5 - + - -
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Residues in contact with MET 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 5.6 0.2 - - + -
31J SER* 3.4 39.7 - - - +
34J TYR* 4.5 16.8 - - + -
35J ALA* 4.4 11.9 - - + -
20X LEU* 3.8 29.8 - - + +
24X LEU* 5.1 7.9 - - + -
62X ALA* 3.1 21.9 + - + +
63X GLU* 3.2 23.8 + - + +
65X PHE* 1.3 76.3 - - - +
67X LYS* 1.3 61.3 + - - +
69X GLN* 3.4 4.5 - - - +
70X ASN* 3.3 27.0 + - - -
76X VAL* 3.9 20.7 - - + +
78X LEU* 4.7 7.6 - - + -
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Residues in contact with LYS 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 6.0 0.4 - - - +
34J TYR* 3.4 28.2 + - - +
38J ASP* 3.3 31.5 + - - +
45J HIS* 5.2 4.8 + - - -
49J GLU* 5.8 1.6 - - - -
63X GLU 3.1 10.0 + - - +
64X LYS* 3.6 11.4 - - - +
66X MET* 1.3 78.6 - - - +
68X TYR* 1.3 58.4 + - - +
70X ASN* 3.5 3.3 + - - +
71X LYS* 3.0 44.1 + - + +
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Residues in contact with TYR 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 5.6 0.2 - - - -
8X TYR* 3.9 17.5 - + - -
16X VAL* 4.6 8.3 - - + -
64X LYS 2.9 18.6 + - - +
65X PHE* 3.5 6.3 - - - +
67X LYS* 1.3 73.8 - - - +
69X GLN* 1.3 67.9 + - - +
71X LYS* 3.1 16.8 + - + +
72X ARG* 2.8 53.1 + - + +
124X HIS* 2.8 42.2 + + - -
125X LEU* 3.2 36.8 - - + -
128X PHE* 3.6 42.2 - + + -
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Residues in contact with GLN 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X TYR* 3.0 35.7 + - - -
13X GLU* 3.2 27.5 + - - +
16X VAL* 3.5 13.9 - - + +
17X ASN* 3.4 19.0 + - - -
20X LEU* 5.8 0.8 - - + +
65X PHE 3.0 14.2 + - - +
66X MET* 3.4 6.7 - - - +
68X TYR* 1.3 83.3 - - - +
70X ASN* 1.3 61.3 + - - +
72X ARG* 3.2 5.0 + - - +
73X GLY 3.1 3.3 + - - -
74X GLY* 2.9 44.3 + - - -
75X ARG 4.0 7.0 - - - -
76X VAL* 3.7 23.3 - - + +
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Residues in contact with ASN 70 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 3.3 17.7 - - - +
34J TYR* 6.2 0.6 - - - -
35J ALA* 3.2 28.9 + - - +
38J ASP* 3.0 39.2 + - - +
39J ARG* 3.4 28.0 - - - +
40J ASP* 5.0 3.1 + - - +
4X VAL* 4.5 1.0 - - - +
66X MET 3.3 13.7 + - - -
67X LYS 3.9 3.4 - - - +
69X GLN* 1.3 76.7 - - - +
71X LYS* 1.3 66.0 + - - +
73X GLY* 3.2 10.0 + - - -
74X GLY 3.9 11.6 - - - +
75X ARG* 4.0 1.7 + - - +
76X VAL* 4.6 9.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 2.7 36.8 + - - +
138A VAL* 4.2 26.6 - - + +
139A LYS* 4.5 12.1 - - - +
142A LYS* 4.1 26.9 - - + +
4X VAL* 3.4 17.5 - - - +
67X LYS* 3.0 29.0 + - + +
68X TYR* 3.1 23.0 + - + +
70X ASN* 1.3 76.1 - - - +
72X ARG* 1.3 61.8 + - + +
124X HIS* 5.4 0.2 - - + -
128X PHE* 6.2 2.6 - - - -
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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