Contacts of the helix formed by residues 45 - 71 (chain V) 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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L LYS* 5.1 4.5 + - - -
142M LYS* 3.9 9.9 - - - -
146M ASP* 3.0 34.3 + - + -
150M ASN* 5.8 0.4 - - - -
37V PHE 4.6 1.6 - - - -
38V ASP* 3.4 36.8 + - - -
43V ALA* 3.3 15.6 + - + -
44V LEU* 1.3 69.2 - - - +
46V ASN* 1.3 65.2 + - - +
48V ALA* 3.5 6.9 - - - +
49V GLU* 3.1 30.0 + - - +
167V ASP* 3.6 3.6 + - - +
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Residues in contact with ASN 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V HIS* 1.3 78.0 - - - +
47V VAL* 1.3 66.1 + - - +
49V GLU* 3.3 8.5 + - - +
50V PHE 3.0 17.7 + - - -
167V ASP* 3.0 45.8 + - - +
168V LYS* 4.4 10.9 - - - +
171V VAL* 3.2 28.5 - - + +
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Residues in contact with VAL 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V PHE* 3.9 20.4 - - + -
44V LEU* 3.5 18.6 - - + +
45V HIS 3.3 0.2 - - - -
46V ASN* 1.3 76.4 - - - +
48V ALA* 1.3 61.8 + - - +
50V PHE* 3.2 9.3 + - - +
51V PHE* 3.2 44.7 + - + -
92V THR* 4.1 26.2 - - + +
96V MET* 4.6 4.5 - - + -
163V GLU 5.8 0.2 - - - +
166V PHE* 4.3 13.5 - - + -
167V ASP* 3.1 22.6 + - + +
171V VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V TYR* 3.2 39.6 - - + +
37V PHE* 3.7 24.7 - - + +
38V ASP* 4.1 4.3 - - + +
44V LEU 3.0 13.6 + - - +
45V HIS* 3.5 15.9 - - - +
46V ASN 3.2 0.2 - - - -
47V VAL* 1.3 78.4 - - - +
49V GLU* 1.3 58.4 + - - +
51V PHE* 3.4 2.2 + - - -
52V LYS 3.0 21.0 + - - -
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Residues in contact with GLU 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L LYS* 5.8 1.6 - - - -
34V TYR* 3.6 22.9 + - - -
45V HIS* 3.1 19.3 + - + +
46V ASN* 3.3 11.2 + - - +
48V ALA* 1.3 74.0 - - - +
50V PHE* 1.3 60.5 + - - +
52V LYS* 3.3 25.0 + - - +
53V GLU* 2.9 40.7 + - - +
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Residues in contact with PHE 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V TYR* 5.9 0.2 - + - -
46V ASN 3.0 13.8 + - - +
47V VAL* 3.3 10.1 - - - +
49V GLU* 1.3 76.9 - - - +
51V PHE* 1.3 92.5 + + - +
53V GLU* 3.5 8.4 + - + +
54V HIS* 3.2 54.1 + + - -
96V MET* 4.0 21.1 - - + -
143V ARG* 3.9 18.6 - - - -
144V ILE* 4.5 11.9 - - + -
147V PHE* 3.7 28.0 - + - -
171V VAL* 3.7 20.4 - - + +
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Residues in contact with PHE 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V TYR* 3.6 48.8 - + - +
33V MET* 3.8 29.4 - - + -
34V TYR 4.0 4.7 - - - +
37V PHE* 3.7 22.4 - + - -
47V VAL* 3.2 37.5 + - + -
48V ALA* 3.9 5.2 - - - +
50V PHE* 1.3 97.9 - + - +
52V LYS* 1.3 59.8 + - - +
54V HIS* 3.2 5.4 + - + +
55V SER* 2.9 23.9 + - - -
95V ALA* 4.1 12.1 - - + -
96V MET* 3.7 24.0 - - + -
99V ALA* 4.2 8.7 - - + -
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Residues in contact with LYS 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L GLU* 3.6 24.2 + - - +
34V TYR* 3.7 39.7 + - + +
48V ALA 3.0 18.2 + - - +
49V GLU* 3.6 33.3 + - - +
50V PHE 3.3 0.2 - - - -
51V PHE* 1.3 76.5 - - - +
53V GLU* 1.3 63.4 + - + +
55V SER* 3.2 20.8 + - - +
56V HIS* 3.3 29.1 + - + +
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Residues in contact with GLU 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49V GLU* 2.9 26.1 + - + +
50V PHE* 3.6 8.5 - - + +
52V LYS* 1.3 77.9 - - + +
54V HIS* 1.3 63.1 + - + +
56V HIS* 3.3 10.0 + - - +
57V GLU* 3.1 36.0 + - - +
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Residues in contact with HIS 54 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V TYR* 3.9 23.2 - + + -
50V PHE* 3.2 41.0 + + - +
51V PHE* 3.2 10.5 + - - +
53V GLU* 1.3 81.6 - - + +
55V SER* 1.3 64.1 + - - +
57V GLU* 3.4 16.7 + - - +
58V GLU* 3.2 32.6 + - - +
103V GLU* 3.6 17.7 + - - -
140V ASP* 3.7 26.9 - - + -
143V ARG* 3.1 27.7 + - - -
144V ILE* 4.9 4.7 - - + -
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Residues in contact with SER 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L GLU* 4.5 4.3 + - - -
27V SER* 2.9 47.6 + - - +
30V TYR* 3.7 14.3 - - - +
31V SER* 3.8 15.2 + - - -
51V PHE 2.9 9.5 + - - -
52V LYS* 3.2 16.6 + - - +
53V GLU 3.3 0.2 - - - -
54V HIS* 1.3 74.2 - - - +
56V HIS* 1.3 75.8 + - - +
58V GLU 3.4 1.0 + - - -
59V ARG* 3.1 11.6 + - - +
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Residues in contact with HIS 56 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L ARG* 6.0 3.3 - - + +
63L GLU* 3.0 34.5 + - - -
52V LYS* 3.4 29.6 + - + +
53V GLU* 3.3 12.8 + - - +
54V HIS 3.2 0.4 - - - -
55V SER* 1.3 91.2 + - - +
57V GLU* 1.3 56.9 + - + +
59V ARG* 3.5 8.0 + - + +
60V GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 57 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V GLU* 3.1 20.5 + - - +
54V HIS* 3.6 26.1 + - - +
55V SER 3.2 0.2 - - - -
56V HIS* 1.3 75.4 - - - +
58V GLU* 1.3 64.5 + - + +
60V GLU* 3.2 7.6 + - + +
61V HIS* 2.9 45.9 + - + +
140V ASP* 4.1 17.5 - - - +
143V ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V GLU* 2.7 30.9 - - - +
26V ALA* 4.2 9.0 - - + -
27V SER* 3.8 12.6 - - - +
30V TYR* 4.0 17.0 - - + -
54V HIS* 3.2 21.0 + - - +
57V GLU* 1.3 80.9 - - - +
59V ARG* 1.3 57.5 + - - +
61V HIS* 3.1 10.7 + - - +
62V ALA* 3.0 25.5 + - - +
103V GLU* 3.4 14.9 - - - +
106V VAL* 4.9 1.1 - - - +
176V MG 2.0 32.5 - - - -
177V MG 2.6 25.3 - - - -
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Residues in contact with ARG 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L HIS* 6.1 2.2 - - + +
59L ARG* 5.7 9.2 - - + -
24V LEU* 4.9 11.4 - - + -
27V SER* 3.6 13.2 + - - +
55V SER 3.1 17.4 + - - +
56V HIS* 3.6 9.9 - - + +
57V GLU 3.1 0.2 - - - -
58V GLU* 1.3 74.8 - - - +
60V GLU* 1.3 64.2 + - - +
62V ALA* 3.2 8.5 + - - +
63V GLU* 3.1 36.3 + - + +
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V HIS 3.1 15.5 + - - +
57V GLU* 3.2 11.0 + - + +
59V ARG* 1.3 76.0 - - - +
61V HIS* 1.3 60.5 + - + +
63V GLU* 3.5 11.4 + - - +
64V LYS* 3.1 32.7 + - - +
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Residues in contact with HIS 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V GLU* 3.4 16.1 + - - +
57V GLU* 2.9 30.1 + - + +
58V GLU* 3.1 17.7 + - - +
59V ARG 3.2 0.2 - - - -
60V GLU* 1.3 78.2 - - + +
62V ALA* 1.3 63.3 + - - +
64V LYS* 3.4 19.0 + - - -
65V PHE* 3.3 13.2 + - - -
132V GLU 4.6 7.2 + - - -
133V TYR* 3.0 40.8 + + + -
136V GLU* 5.1 13.7 - - + +
137V GLN* 5.1 1.1 - - - -
140V ASP* 5.6 0.4 - - - -
176V MG 2.7 24.5 - - - -
177V MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V LEU* 3.7 15.6 - - + +
23V GLU* 3.8 9.6 - - + +
24V LEU* 3.7 35.4 - - + -
58V GLU 3.0 11.7 + - - +
59V ARG 3.5 8.3 - - - +
61V HIS* 1.3 76.7 - - - +
63V GLU* 1.3 64.3 + - + +
65V PHE* 3.3 8.8 + - - +
66V MET* 3.1 26.6 + - + +
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Residues in contact with GLU 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L SER* 4.8 5.1 + - - +
34L TYR* 5.1 11.2 + - + -
52L LYS* 3.7 20.7 + - - +
55L SER* 4.4 5.5 + - - -
56L HIS* 3.1 34.8 + - - -
24V LEU* 6.4 0.2 - - + -
59V ARG* 3.1 25.8 + - + +
60V GLU* 3.8 12.3 - - - +
61V HIS 3.3 0.2 - - - -
62V ALA* 1.3 76.1 - - + +
64V LYS* 1.3 64.2 + - - +
66V MET* 3.2 24.4 + - + +
67V LYS* 3.1 24.3 + - - +
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Residues in contact with LYS 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60V GLU* 3.1 20.0 + - - +
61V HIS* 3.6 18.2 + - - +
62V ALA 3.3 0.6 - - - -
63V GLU* 1.3 75.5 - - - +
65V PHE* 1.3 57.8 + - - +
67V LYS* 3.5 7.9 + - - +
68V TYR* 2.9 27.5 + - - +
128V PHE* 3.7 9.3 - - + -
132V GLU* 2.9 52.9 + - + +
133V TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V VAL* 3.9 29.9 - - + +
19V MET* 3.4 33.2 - - + -
20V LEU* 4.2 19.0 - - + +
23V GLU* 4.1 15.3 - - + -
61V HIS 3.3 16.7 + - - -
62V ALA 3.3 8.0 + - - +
63V GLU 3.2 0.6 - - - -
64V LYS* 1.3 78.2 - - - +
66V MET* 1.3 64.6 + - - +
68V TYR* 3.5 3.5 - - + +
69V GLN* 3.0 24.3 + - - +
110V LEU* 4.0 11.0 - - + -
113V LEU* 4.5 7.4 - - + -
125V LEU* 5.3 0.4 - - + -
128V PHE* 3.5 25.6 - + - -
129V LEU* 4.0 11.9 - - + -
133V TYR* 3.4 32.3 - + - -
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Residues in contact with MET 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 5.5 0.2 - - + -
31L SER* 3.3 39.3 - - - +
34L TYR* 4.6 15.0 - - + -
35L ALA* 4.3 13.9 - - + -
20V LEU* 3.8 29.1 - - + +
24V LEU* 5.1 7.9 - - + -
62V ALA* 3.1 22.2 + - + +
63V GLU* 3.2 22.6 + - + +
65V PHE* 1.3 76.0 - - - +
67V LYS* 1.3 62.1 + - - +
69V GLN* 3.4 4.9 - - - +
70V ASN* 3.3 26.3 + - - -
76V VAL* 3.9 20.3 - - + +
78V LEU* 4.7 7.9 - - + -
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Residues in contact with LYS 67 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 6.0 0.4 - - - +
34L TYR* 3.3 30.2 + - - +
38L ASP* 3.1 33.0 + - - +
45L HIS* 5.0 5.7 + - - -
49L GLU* 5.8 1.6 - - - -
63V GLU 3.1 9.8 + - - +
64V LYS* 3.6 11.9 - - - +
66V MET* 1.3 78.4 - - - +
68V TYR* 1.3 57.5 + - - +
70V ASN* 3.5 3.1 + - - +
71V LYS* 3.0 44.8 + - + +
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Residues in contact with TYR 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLU* 5.7 0.2 - - - -
8V TYR* 3.9 17.5 - + - -
16V VAL* 4.6 8.3 - - + -
64V LYS 2.9 17.7 + - - +
65V PHE* 3.5 6.5 - - - +
66V MET 3.2 0.2 - - - -
67V LYS* 1.3 75.5 - - - +
69V GLN* 1.3 67.0 + - - +
71V LYS* 3.1 17.3 + - + +
72V ARG* 2.8 52.6 + - + +
124V HIS* 2.8 42.0 + + - -
125V LEU* 3.2 35.8 - - + -
128V PHE* 3.6 44.0 - + + -
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Residues in contact with GLN 69 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V TYR* 3.0 36.7 + - - -
13V GLU* 3.2 27.8 + - - +
16V VAL* 3.5 14.8 - - + +
17V ASN* 3.4 18.8 + - - -
20V LEU* 5.8 0.6 - - + +
65V PHE 3.0 14.0 + - - +
66V MET* 3.4 6.5 - - - +
68V TYR* 1.3 83.1 - - - +
70V ASN* 1.3 60.9 + - - +
72V ARG* 3.2 4.7 + - - +
73V GLY 3.1 4.0 + - - -
74V GLY* 2.9 42.7 + - - -
75V ARG 4.0 7.0 - - - -
76V VAL* 3.7 23.8 - - + +
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Residues in contact with ASN 70 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 3.3 16.8 - - - +
34L TYR* 6.3 0.2 - - - -
35L ALA* 3.0 30.1 + - - +
38L ASP* 3.2 39.5 + - - +
39L ARG* 3.3 27.9 - - - +
40L ASP* 4.9 3.8 + - - +
4V VAL* 4.5 0.7 - - - +
66V MET 3.3 13.5 + - - +
67V LYS 3.9 2.9 - - - +
69V GLN* 1.3 76.6 - - - +
71V LYS* 1.3 65.3 + - - +
73V GLY* 3.2 10.4 + - - -
74V GLY 3.9 11.8 - - - +
75V ARG* 4.0 2.1 + - - +
76V VAL* 4.6 9.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLU* 2.8 36.6 + - - +
138E VAL* 4.3 25.1 - - + +
139E LYS* 4.6 11.2 - - - +
142E LYS* 4.1 27.4 - - + +
4V VAL* 3.4 17.8 - - - +
67V LYS* 3.0 29.6 + - + +
68V TYR* 3.1 21.7 + - + +
70V ASN* 1.3 76.8 - - - +
72V ARG* 1.3 64.1 + - + +
128V 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