Contacts of the helix formed by residues 45 - 71 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N PHE 4.6 1.6 - - - -
38N ASP* 3.4 37.4 + - - -
43N ALA* 3.3 14.4 + - + -
44N LEU* 1.3 70.2 - - - +
46N ASN* 1.3 63.8 + - - +
48N ALA* 3.5 6.9 - - - +
49N GLU* 3.1 30.9 + - + +
167N ASP* 3.6 3.2 + - - +
67R LYS* 5.0 4.7 + - - -
142S LYS* 3.9 10.3 - - - -
146S ASP* 3.0 34.9 + - + -
150S ASN* 5.8 0.2 - - - -
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Residues in contact with ASN 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N HIS* 1.3 78.1 - - - +
47N VAL* 1.3 65.9 + - - +
49N GLU* 3.3 9.4 + - - +
50N PHE 3.0 17.7 + - - -
167N ASP* 3.0 46.2 + - - +
168N LYS* 4.4 11.3 - - - +
171N VAL* 3.2 28.0 - - + +
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Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N PHE* 3.9 20.4 - - + -
44N LEU* 3.5 18.4 - - + +
46N ASN* 1.3 77.7 - - - +
48N ALA* 1.3 61.9 + - - +
50N PHE* 3.2 8.5 + - - +
51N PHE* 3.2 45.5 + - + -
92N THR* 4.1 26.5 - - + +
96N MET* 4.6 4.7 - - + -
163N GLU 5.8 0.2 - - - +
166N PHE* 4.3 13.5 - - + -
167N ASP* 3.1 23.4 + - + +
171N VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 3.2 40.2 - - + +
37N PHE* 3.7 24.2 - - + +
38N ASP* 4.1 4.3 - - + +
44N LEU 3.0 14.3 + - - +
45N HIS* 3.5 15.3 - - - +
47N VAL* 1.3 77.6 - - - +
49N GLU* 1.3 58.8 + - - +
51N PHE* 3.4 2.1 + - - -
52N LYS 3.0 20.6 + - - -
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Residues in contact with GLU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 3.6 23.4 + - - -
45N HIS* 3.1 18.8 + - + +
46N ASN* 3.3 12.1 + - - +
48N ALA* 1.3 73.6 - - - +
50N PHE* 1.3 61.1 + - - +
52N LYS* 3.6 24.3 + - - +
53N GLU* 2.9 39.3 + - - +
67R LYS* 5.7 2.1 - - - -
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Residues in contact with PHE 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 5.9 0.4 - + - -
46N ASN 3.0 13.8 + - - +
47N VAL* 3.2 10.3 + - - +
49N GLU* 1.3 76.1 - - - +
51N PHE* 1.3 92.8 + + - +
53N GLU* 3.5 8.8 + - + +
54N HIS* 3.2 55.8 + + - -
96N MET* 4.0 20.9 - - + -
143N ARG* 3.9 17.9 - - - -
144N ILE* 4.5 11.9 - - + -
147N PHE* 3.7 29.4 - + - -
171N VAL* 3.7 20.6 - - + -
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Residues in contact with PHE 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.6 49.7 - + + +
33N MET* 3.8 29.4 - - + -
34N TYR 4.0 4.7 - - - +
37N PHE* 3.7 22.2 - + - -
47N VAL* 3.2 36.6 + - + -
48N ALA* 3.9 5.6 - - - +
50N PHE* 1.3 99.2 - + - +
52N LYS* 1.3 58.7 + - - +
54N HIS* 3.2 5.4 + - + +
55N SER* 2.9 23.9 + - - -
92N THR 5.7 0.2 - - - -
95N ALA* 4.1 12.1 - - + -
96N MET* 3.7 23.8 - - + -
99N ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 3.7 38.1 + - + +
48N ALA 3.0 17.8 + - - +
49N GLU* 3.6 33.3 + - - +
50N PHE 3.3 0.4 - - - -
51N PHE* 1.3 76.3 - - - +
53N GLU* 1.3 63.2 + - + +
55N SER* 3.2 21.7 + - - +
56N HIS* 3.3 29.9 + - + +
63R GLU* 3.6 24.4 + - - +
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Residues in contact with GLU 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N GLU* 2.9 25.8 + - + +
50N PHE* 3.6 9.3 - - + +
52N LYS* 1.3 78.4 - - + +
54N HIS* 1.3 63.5 + - + +
56N HIS* 3.3 10.2 + - - +
57N GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.9 23.9 - + + -
50N PHE* 3.2 41.0 + + - +
51N PHE* 3.2 11.2 + - - +
53N GLU* 1.3 82.9 - - + +
55N SER* 1.3 63.0 + - - +
57N GLU* 3.4 18.8 + - - +
58N GLU* 3.2 32.1 + - - +
103N GLU* 3.6 17.8 + - - -
140N ASP* 3.7 25.8 - - + -
143N ARG* 3.1 27.1 + - - -
144N ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N SER* 2.9 47.3 + - - +
30N TYR* 3.7 14.6 - - - +
31N SER* 3.8 14.3 + - - -
51N PHE 2.9 9.8 + - - -
52N LYS* 3.2 16.6 + - - +
53N GLU 3.3 0.2 - - - -
54N HIS* 1.3 73.4 - - - +
56N HIS* 1.3 77.3 + - - +
58N GLU 3.4 1.0 + - - -
59N ARG* 3.1 12.2 + - - +
63R GLU* 4.4 4.9 + - - -
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Residues in contact with HIS 56 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N LYS* 3.4 28.3 + - + +
53N GLU* 3.5 11.9 - - - +
54N HIS 3.2 0.6 - - - -
55N SER* 1.3 90.0 + - - +
57N GLU* 1.3 56.1 + - - +
59N ARG* 3.5 7.4 + - + +
60N GLU* 3.1 25.8 + - - +
59R ARG* 6.0 2.7 - - + +
63R GLU* 3.0 36.0 + - - -
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Residues in contact with GLU 57 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N GLU* 3.1 21.1 + - - +
54N HIS* 3.6 25.3 + - - +
55N SER 3.2 0.2 - - - -
56N HIS* 1.3 75.6 - - - +
58N GLU* 1.3 62.8 + - + +
60N GLU* 3.2 7.6 + - + +
61N HIS* 2.9 46.8 + - + +
140N ASP* 4.1 18.0 - - - +
143N ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N GLU* 2.7 30.0 - - - +
26N ALA* 4.2 9.4 - - + -
27N SER* 3.8 13.2 - - - +
30N TYR* 4.0 16.8 - - + -
54N HIS* 3.2 20.6 + - - +
57N GLU* 1.3 80.4 - - - +
59N ARG* 1.3 58.2 + - - +
61N HIS* 3.1 10.0 + - - +
62N ALA* 3.0 26.5 + - - +
103N GLU* 3.4 14.3 - - - +
106N VAL* 4.9 0.6 - - - +
176N MG 2.0 32.7 - - - -
177N MG 2.6 25.2 - - - -
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Residues in contact with ARG 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N LEU* 4.9 11.4 - - + -
27N SER* 3.6 13.1 + - - +
55N SER 3.1 18.2 + - - +
56N HIS* 3.6 9.0 - - + +
57N GLU 3.1 0.2 - - - -
58N GLU* 1.3 74.3 - - - +
60N GLU* 1.3 65.5 + - - +
62N ALA* 3.2 8.1 + - - +
63N GLU* 3.1 37.1 + - + +
56R HIS* 6.0 3.1 - - + +
59R ARG* 5.6 9.6 - - + -
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Residues in contact with GLU 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N HIS 3.1 15.1 + - - +
57N GLU* 3.2 11.2 + - - +
59N ARG* 1.3 76.1 - - - +
61N HIS* 1.3 59.5 + - + +
63N GLU* 3.5 12.5 + - - +
64N LYS* 3.1 33.3 + - - +
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Residues in contact with HIS 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N GLU* 3.4 15.7 - - - +
57N GLU* 2.9 30.6 + - + +
58N GLU* 3.1 17.2 + - - +
59N ARG 3.2 0.2 - - - -
60N GLU* 1.3 79.1 - - + +
62N ALA* 1.3 64.3 + - - +
64N LYS* 4.4 18.4 + - - +
65N PHE* 3.3 13.4 + - - -
132N GLU 4.6 6.9 + - - -
133N TYR* 3.0 39.5 + + + -
136N GLU* 5.1 13.9 - - + +
137N GLN* 5.1 0.9 - - - -
140N ASP* 5.6 0.4 - - - -
176N MG 2.7 24.2 - - - -
177N MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 3.7 16.8 - - + +
23N GLU* 3.8 9.2 - - + +
24N LEU* 3.7 34.5 - - + -
58N GLU 3.0 11.5 + - - +
59N ARG 3.5 9.0 - - - +
61N HIS* 1.3 76.8 - - - +
63N GLU* 1.3 63.7 + - + +
65N PHE* 3.3 8.9 + - - +
66N MET* 3.1 26.2 + - + +
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Residues in contact with GLU 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N LEU* 6.4 0.4 - - + -
59N ARG* 3.1 24.4 + - + +
60N GLU* 3.8 11.2 - - - +
61N HIS 3.3 0.2 - - - -
62N ALA* 1.3 76.1 - - + +
64N LYS* 1.3 64.2 + - - +
66N MET* 3.2 25.6 + - + +
67N LYS* 3.1 24.8 + - - +
31R SER* 4.9 5.1 + - - +
34R TYR* 5.1 9.9 - - + -
52R LYS* 3.7 19.7 - - - +
55R SER* 4.4 5.5 + - - -
56R HIS* 3.0 35.8 + - - -
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Residues in contact with LYS 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N GLU* 3.1 21.0 + - - +
61N HIS* 3.6 17.4 - - - +
62N ALA 3.3 0.2 - - - -
63N GLU* 1.3 75.5 - - - +
65N PHE* 1.3 56.9 + - - +
67N LYS* 3.5 8.4 + - - +
68N TYR* 2.9 27.0 + - - +
128N PHE* 3.7 9.8 - - + -
132N GLU* 2.9 53.1 + - + +
133N TYR* 3.2 21.5 - - + +
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Residues in contact with PHE 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N VAL* 3.9 28.8 - - + +
19N MET* 3.4 33.0 - - + -
20N LEU* 4.2 18.6 - - + -
23N GLU* 4.1 14.8 - - + -
61N HIS 3.3 17.1 + - - -
62N ALA 3.3 8.7 + - - +
63N GLU 3.2 0.4 - - - -
64N LYS* 1.3 78.8 - - - +
66N MET* 1.3 64.5 + - - +
68N TYR* 3.3 3.1 + - + +
69N GLN* 3.0 24.6 + - - +
110N LEU* 4.0 11.2 - - + -
113N LEU* 4.5 7.6 - - + -
125N LEU* 5.3 0.2 - - + -
128N PHE* 3.5 25.6 - + - -
129N LEU* 4.0 12.3 - - + -
133N TYR* 3.4 31.0 - + - -
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Residues in contact with MET 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 3.8 30.1 - - + -
24N LEU* 5.1 7.6 - - + -
62N ALA* 3.1 20.2 + - + +
63N GLU* 3.2 22.4 + - + +
65N PHE* 1.3 76.2 - - - +
67N LYS* 1.3 61.8 + - - +
69N GLN* 3.4 4.3 - - - +
70N ASN* 3.3 27.0 + - - -
76N VAL* 3.9 22.0 - - + +
78N LEU* 4.7 7.4 - - + -
28R TYR* 5.5 0.2 - - + -
31R SER* 3.3 41.1 - - - +
34R TYR* 4.5 14.8 - - + -
35R ALA* 4.3 13.5 - - + -
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Residues in contact with LYS 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 6.1 0.2 - - - +
63N GLU 3.1 9.1 + - - +
64N LYS* 3.6 11.4 - - - +
66N MET* 1.3 78.8 - - - +
68N TYR* 1.3 57.7 + - - +
70N ASN* 3.5 2.8 + - - +
71N LYS* 3.0 44.3 + - + +
34R TYR* 3.3 30.0 + - - +
38R ASP* 3.1 34.1 + - - +
45R HIS* 5.0 5.3 + - - -
49R GLU* 5.7 1.8 - - - -
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Residues in contact with TYR 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLU* 5.6 0.2 - - - -
8N TYR* 3.9 18.2 - + - -
16N VAL* 4.6 8.1 - - + -
64N LYS 2.9 18.1 + - - +
65N PHE* 3.5 6.7 - - - +
66N MET 3.2 0.2 - - - -
67N LYS* 1.3 74.3 - - - +
69N GLN* 1.3 68.0 + - - +
71N LYS* 3.1 17.0 + - + +
72N ARG* 2.8 52.2 + - + +
124N HIS* 2.8 42.0 + + - -
125N LEU* 3.2 35.9 - - + -
128N PHE* 3.6 43.1 - + + -
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Residues in contact with GLN 69 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N TYR* 3.0 36.6 + - - -
13N GLU* 3.2 28.0 + - - +
16N VAL* 3.5 14.5 - - + +
17N ASN* 3.4 18.6 + - - -
20N LEU* 6.0 0.7 - - + -
65N PHE 3.0 14.0 + - - +
66N MET 3.4 7.2 - - - +
68N TYR* 1.3 82.9 - - - +
70N ASN* 1.3 61.1 + - - +
72N ARG* 3.2 4.7 + - - +
73N GLY 3.1 3.8 + - - -
74N GLY* 2.9 42.5 + - - -
75N ARG 4.0 7.0 - - - -
76N VAL* 3.7 24.9 - - + +
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Residues in contact with ASN 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 3.3 16.7 - - - +
4N VAL* 4.5 1.0 - - - +
66N MET 3.3 12.9 + - - -
67N LYS 3.9 2.9 - - - +
69N GLN* 1.3 76.5 - - - +
71N LYS* 1.3 64.9 + - - +
73N GLY* 3.2 10.0 + - - -
74N GLY 3.9 12.1 - - - +
75N ARG* 4.0 1.0 + - - +
76N VAL* 4.6 9.3 + - - +
34R TYR* 6.3 0.2 - - - -
35R ALA* 3.0 30.7 + - - +
38R ASP* 3.2 39.7 + - - +
39R ARG* 3.3 27.5 - - - +
40R ASP* 4.9 3.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLU* 2.8 37.0 + - - +
138J VAL* 4.3 24.7 - - + +
139J LYS* 4.6 11.9 - - - +
142J LYS* 4.1 27.3 - - + +
4N VAL* 3.4 18.2 - - - +
67N LYS* 3.0 29.6 + - + +
68N TYR* 3.1 22.1 + - + +
70N ASN* 1.3 76.3 - - - +
72N ARG* 1.3 64.1 + - + +
128N 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