Contacts of the helix formed by residues 45 - 71 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 5.0 4.9 + - - -
37H PHE 4.6 1.6 - - - -
38H ASP* 3.4 44.9 + - - +
43H ALA* 3.3 15.7 + - + -
44H LEU* 1.3 68.8 - - - +
46H ASN* 1.3 65.7 + - - +
48H ALA* 3.5 7.0 - - - +
49H GLU* 3.1 30.8 + - + +
167H ASP* 3.6 3.0 + - - +
142I LYS* 4.0 2.2 - - - -
146I ASP* 3.1 33.9 + - + -
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Residues in contact with ASN 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H HIS* 1.3 77.7 - - - +
47H VAL* 1.3 65.7 + - - +
49H GLU* 3.3 8.8 + - - +
50H PHE 3.0 17.7 + - - -
167H ASP* 3.0 46.0 + - - +
168H LYS* 4.4 10.5 - - - +
171H VAL* 3.2 27.8 - - + +
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.9 21.1 - - + -
44H LEU* 3.5 18.4 - - + +
45H HIS 3.3 0.2 - - - -
46H ASN* 1.3 75.7 - - - +
48H ALA* 1.3 61.5 + - - +
50H PHE* 3.2 8.8 + - - +
51H PHE* 3.2 45.1 + - + -
92H THR* 4.1 26.2 - - + +
96H MET* 4.6 4.7 - - + -
166H PHE* 4.3 13.5 - - + -
167H ASP* 3.1 22.5 + - + +
171H VAL* 4.6 5.2 - - + -
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H TYR* 3.2 40.2 - - + +
37H PHE* 3.7 24.7 - - + +
38H ASP* 4.1 4.0 - - + +
44H LEU 3.0 13.7 + - - +
45H HIS* 3.5 15.3 - - - +
47H VAL* 1.3 78.4 - - - +
49H GLU* 1.3 57.8 + - - +
51H PHE* 3.4 2.3 + - - -
52H LYS 3.0 21.7 + - - -
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 5.8 1.7 - - - -
34H TYR* 3.6 23.6 + - - -
45H HIS* 3.1 18.8 + - + +
46H ASN* 3.3 10.7 + - - +
48H ALA* 1.3 73.8 - - - +
50H PHE* 1.3 60.2 + - - +
52H LYS* 3.6 25.2 + - - +
53H GLU* 2.9 39.0 + - - +
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Residues in contact with PHE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 5.9 0.4 - + - -
46H ASN 3.0 13.4 + - - +
47H VAL* 3.2 10.1 + - - +
49H GLU* 1.3 76.7 - - - +
51H PHE* 1.3 94.6 + + - +
53H GLU* 3.5 7.6 + - + +
54H HIS* 3.2 54.5 + + - -
96H MET* 4.0 20.2 - - + -
143H ARG* 3.9 17.9 - - - -
144H ILE* 4.5 11.9 - - + -
147H PHE* 3.7 28.7 - + - -
171H VAL* 3.7 21.5 - - + +
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Residues in contact with PHE 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 3.6 49.9 - + - +
33H MET* 3.8 28.9 - - + -
34H TYR 4.0 4.7 - - - +
37H PHE* 3.7 22.4 - + - -
47H VAL* 3.2 37.2 + - + -
48H ALA* 3.9 5.4 - - - +
49H GLU 3.2 0.2 - - - -
50H PHE* 1.3 98.0 - + - +
52H LYS* 1.3 59.0 + - - +
54H HIS* 3.2 4.9 + - + +
55H SER* 2.9 24.1 + - - -
95H ALA* 4.1 12.6 - - + -
96H MET* 3.7 24.5 - - + -
99H ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU* 3.6 24.6 + - - +
34H TYR* 3.7 37.7 + - + +
48H ALA 3.0 17.6 + - - +
49H GLU* 3.6 33.1 + - - +
50H PHE 3.3 0.2 - - - -
51H PHE* 1.3 75.9 - - - +
53H GLU* 1.3 63.9 + - + +
55H SER* 3.2 21.6 + - - +
56H HIS* 3.3 29.3 + - + +
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Residues in contact with GLU 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLU* 2.9 24.3 + - + +
50H PHE* 3.6 9.2 - - + +
52H LYS* 1.3 78.5 - - + +
54H HIS* 1.3 64.9 + - + +
56H HIS* 3.3 10.6 + - - +
57H GLU* 3.1 36.6 + - - +
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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
----------------------------------------------------------
30H TYR* 3.9 23.2 - + + -
50H PHE* 3.2 41.6 + + - +
51H PHE* 3.2 10.5 + - - +
53H GLU* 1.3 80.7 - - + +
55H SER* 1.3 63.3 + - - +
57H GLU* 3.4 17.4 + - - +
58H GLU* 3.2 33.0 + - - +
103H GLU* 3.6 17.8 + - - -
140H ASP* 3.7 25.8 - - + -
143H ARG* 3.1 27.1 + - - -
144H ILE* 4.9 4.7 - - + -
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Residues in contact with SER 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU* 4.4 5.4 + - - -
27H SER* 2.9 47.6 + - - +
30H TYR* 3.7 14.1 - - - +
31H SER* 3.8 14.5 - - - -
34H TYR* 5.8 0.2 - - - +
51H PHE 2.9 9.2 + - - -
52H LYS* 3.2 16.3 + - - +
53H GLU 3.3 0.2 - - - -
54H HIS* 1.3 74.2 - - - +
56H HIS* 1.3 76.5 + - - +
57H GLU 3.3 0.2 + - - -
58H GLU 3.4 0.9 + - - -
59H ARG* 3.1 11.5 + - - +
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Residues in contact with HIS 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ARG* 6.0 3.3 - - + +
63D GLU* 3.0 35.3 + - - -
52H LYS* 3.4 28.5 + - + +
53H GLU* 3.3 12.1 + - - +
54H HIS 3.2 0.2 - - - -
55H SER* 1.3 90.7 + - - +
57H GLU* 1.3 56.5 - - - +
59H ARG* 3.5 7.6 + - + +
60H GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLU* 3.1 20.9 + - - +
54H HIS* 3.6 26.2 + - - +
56H HIS* 1.3 76.7 - - + +
58H GLU* 1.3 64.7 + - + +
60H GLU* 3.2 7.3 + - - +
61H HIS* 3.0 46.3 + - + +
140H ASP* 4.1 18.2 - - - +
143H ARG* 5.8 1.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLU* 2.7 31.0 - - - +
26H ALA* 4.2 8.7 - - + -
27H SER* 3.8 12.8 - - - +
30H TYR* 4.0 17.7 - - + -
54H HIS* 3.2 20.5 + - - +
57H GLU* 1.3 80.0 - - - +
59H ARG* 1.3 58.0 + - - +
61H HIS* 3.1 10.8 + - - +
62H ALA* 3.0 26.2 + - - +
103H GLU* 3.4 14.9 - - - +
106H VAL* 4.9 1.0 - - - +
176H MG 2.0 32.9 - - - -
177H MG 2.6 24.3 - - - -
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Residues in contact with ARG 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D HIS* 6.0 2.5 - - + +
59D ARG* 5.7 8.5 - - + -
24H LEU* 4.9 11.9 - - + -
27H SER* 3.6 13.4 + - - +
55H SER 3.1 18.0 + - - +
56H HIS* 3.6 10.3 - - + +
57H GLU 3.1 0.2 - - - -
58H GLU* 1.3 74.4 - - - +
60H GLU* 1.3 62.7 + - - +
62H ALA* 3.2 8.4 + - - +
63H GLU* 3.1 36.2 + - + +
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Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H HIS 3.1 15.1 + - - +
57H GLU* 3.2 10.7 + - + +
59H ARG* 1.3 75.5 - - - +
61H HIS* 1.3 59.9 + - + +
63H GLU* 3.5 12.0 + - - +
64H LYS* 3.1 32.6 + - - +
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Residues in contact with HIS 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLU* 3.4 15.5 - - - +
57H GLU* 3.0 31.0 + - + +
58H GLU* 3.1 18.4 + - - +
59H ARG 3.2 0.2 - - - -
60H GLU* 1.3 78.4 - - + +
62H ALA* 1.3 62.8 + - - +
64H LYS* 3.4 18.8 + - - +
65H PHE* 3.3 12.9 + - - -
132H GLU 4.6 7.0 + - - -
133H TYR* 3.0 40.7 + + + -
136H GLU* 5.1 14.1 - - + +
137H GLN* 5.1 1.3 - - - -
140H ASP* 5.6 0.4 - - - -
176H MG 2.7 24.3 - - - -
177H MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 3.7 16.6 - - + +
23H GLU* 3.8 9.6 - - + +
24H LEU* 3.7 35.2 - - + -
58H GLU 3.0 12.0 + - - +
59H ARG 3.2 8.9 + - - +
61H HIS* 1.3 76.6 - - - +
63H GLU* 1.3 63.1 + - + +
65H PHE* 3.3 8.9 + - - +
66H MET* 3.1 26.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D SER* 4.8 5.5 + - - +
34D TYR* 5.1 10.1 - - + -
52D LYS* 3.6 20.5 - - - +
55D SER* 4.4 5.9 + - - -
56D HIS* 3.1 33.2 + - - -
24H LEU* 6.4 0.2 - - + -
59H ARG* 3.1 24.4 + - + +
60H GLU* 3.8 12.2 - - - +
62H ALA* 1.3 75.3 - - + +
64H LYS* 1.3 65.6 + - - +
66H MET* 3.2 25.2 + - + +
67H LYS* 3.1 24.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H GLU* 3.1 21.0 + - - +
61H HIS* 3.6 17.2 + - - +
62H ALA 3.3 0.4 - - - -
63H GLU* 1.3 75.9 - - - +
65H PHE* 1.3 58.9 + - - +
67H LYS* 3.5 7.3 + - - +
68H TYR* 2.9 27.0 + - - +
128H PHE* 3.7 9.3 - - + -
132H GLU* 2.9 51.7 + - + +
133H TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL* 3.9 29.5 - - + +
19H MET* 3.4 33.2 - - + -
20H LEU* 4.2 18.3 - - + +
23H GLU* 4.1 15.5 - - + -
61H HIS 3.3 16.5 + - - -
62H ALA 3.3 8.6 + - - +
63H GLU 3.2 0.6 - - - -
64H LYS* 1.3 77.2 - - - +
66H MET* 1.3 64.2 + - - +
68H TYR* 3.5 3.2 - + + +
69H GLN* 3.0 25.1 + - - +
110H LEU* 4.0 11.0 - - + -
113H LEU* 4.5 7.0 - - + -
125H LEU* 5.3 0.4 - - + -
128H PHE* 3.5 24.7 - + - -
129H LEU* 4.0 12.8 - - + -
133H TYR* 3.4 31.2 - + - -
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Residues in contact with MET 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 5.5 0.2 - - + -
31D SER* 3.3 40.2 - - - +
34D TYR* 4.6 14.6 - - + -
35D ALA* 4.3 13.0 - - + -
20H LEU* 3.8 29.4 - - + +
24H LEU* 5.1 8.1 - - + -
62H ALA* 3.1 21.3 + - + +
63H GLU* 3.2 22.9 + - + +
65H PHE* 1.3 75.8 - - - +
67H LYS* 1.3 62.2 + - - +
69H GLN* 3.4 4.9 - - - +
70H ASN* 3.3 27.3 + - - -
76H VAL* 3.9 21.1 - - + +
78H LEU* 4.7 7.9 - - + -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.3 29.6 - - - +
38D ASP* 3.1 34.0 + - - +
45D HIS* 5.0 5.1 + - - -
49D GLU* 5.8 1.3 - - - -
63H GLU 3.1 10.2 + - - +
64H LYS* 3.6 11.4 - - - +
66H MET* 1.3 79.7 - - - +
68H TYR* 1.3 57.2 + - - +
70H ASN* 3.5 3.3 + - - +
71H LYS* 3.0 45.0 + - + +
142X LYS* 5.9 0.8 - - - +
----------------------------------------------------------
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Residues in contact with TYR 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TYR* 3.9 18.2 - + - -
16H VAL* 4.6 7.6 - - + -
64H LYS 2.9 18.5 + - - +
65H PHE* 3.5 6.7 - - - +
67H LYS* 1.3 73.2 - - - +
69H GLN* 1.3 67.6 + - - +
71H LYS* 3.1 16.7 + - + +
72H ARG* 2.8 52.7 + - + +
124H HIS* 2.8 42.3 + + - -
125H LEU* 3.2 36.1 - - + -
128H PHE* 3.6 44.6 - + + -
135X GLU* 5.6 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLN 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TYR* 3.0 36.4 + - - -
13H GLU* 3.2 27.9 + - - +
16H VAL* 3.5 14.4 - - + +
17H ASN* 3.4 18.8 + - - -
20H LEU* 5.8 0.4 - - - +
65H PHE 3.0 13.4 + - - +
66H MET 3.4 6.5 - - - +
68H TYR* 1.3 83.5 - - - +
70H ASN* 1.3 61.0 + - - +
72H ARG* 3.2 4.9 + - - +
73H GLY 3.1 3.8 + - - -
74H GLY* 2.9 42.5 + - - -
75H ARG 4.0 6.7 - - - -
76H VAL* 3.7 24.0 - - + +
----------------------------------------------------------
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Residues in contact with ASN 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ALA* 3.1 30.9 + - - +
38D ASP* 3.2 38.2 + - - +
39D ARG* 3.3 27.8 - - - +
40D ASP* 4.9 3.3 + - - +
4H VAL* 4.5 0.7 - - - +
66H MET 3.3 13.5 + - - +
67H LYS 3.9 3.1 - - - +
69H GLN* 1.3 76.4 - - - +
71H LYS* 1.3 65.6 + - - +
73H GLY* 3.2 10.4 + - - -
74H GLY 3.9 12.0 - - - +
75H ARG* 4.0 1.8 + - - +
76H VAL* 4.6 9.5 + - - +
142X LYS* 3.3 16.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 3.4 17.7 - - - +
67H LYS* 3.0 28.9 + - + +
68H TYR* 3.1 23.6 + - + +
70H ASN* 1.3 75.5 - - - +
72H ARG* 1.3 64.1 + - + +
128H PHE* 6.2 2.4 - - - -
135X GLU* 2.8 36.0 + - - +
138X VAL* 4.3 25.0 - - + +
139X LYS* 4.6 11.6 - - - +
142X LYS* 4.1 28.0 - - + +
----------------------------------------------------------
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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