Contacts of the helix formed by residues 52 - 81 (chain N) in PDB entry 3LEL
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 SER 52 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M ARG* 3.3 21.0 - - - +
78M ILE 3.2 18.0 + - - -
79M ILE* 3.4 23.7 - - - +
80M PRO* 3.5 5.2 - - - +
51N ILE* 1.3 72.3 - - - +
53N SER* 1.3 54.1 + - - +
54N LYS* 4.2 6.2 - - - +
55N ALA* 2.8 29.1 + - - +
56N MET* 2.8 15.3 + - - -
-55S A 3.7 10.1 - - - -
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Residues in contact with SER 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N ILE 3.7 3.2 + - - -
52N SER* 1.3 69.7 - - - +
54N LYS* 1.3 62.0 + - - +
56N MET* 3.3 12.3 - - - +
57N SER* 2.9 26.9 + - - -
-55S A 2.8 37.9 + - - -
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Residues in contact with LYS 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M PRO* 4.4 17.0 - - + -
104M GLN* 5.7 10.3 - - + +
52N SER* 3.0 4.8 - - - +
53N SER* 1.3 83.1 + - - +
55N ALA* 1.3 61.0 + - - +
57N SER* 3.0 22.2 + - - -
58N ILE* 3.0 20.3 + - + +
99P GLY* 5.0 0.2 - - - -
-55S A 4.5 0.2 + - - -
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Residues in contact with ALA 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ILE* 3.3 23.8 - - + +
79M ILE 3.7 2.0 - - - -
80M PRO* 3.3 28.8 - - + +
83M LEU* 3.7 10.6 - - + +
51N ILE* 3.6 7.4 - - + -
52N SER* 2.8 9.4 + - - +
54N LYS* 1.3 71.4 - - - +
56N MET* 1.3 64.1 + - - +
58N ILE* 3.6 9.9 - - - +
59N MET* 3.1 28.6 + - - +
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Residues in contact with MET 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR 4.8 0.4 - - - +
35N ALA* 3.4 51.4 - - + +
38N VAL* 3.8 24.9 - - + -
39N TYR* 4.1 15.0 - - + -
51N ILE* 3.4 36.0 - - + +
52N SER 2.8 10.7 + - - +
53N SER* 3.3 17.5 - - - +
55N ALA* 1.3 73.4 - - - +
57N SER* 1.3 64.2 + - - +
59N MET* 3.1 6.0 + - - +
60N ASN* 2.9 22.8 + - + +
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Residues in contact with SER 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N SER 2.9 14.1 + - - -
54N LYS* 3.0 12.3 + - - -
56N MET* 1.3 73.7 - - - +
58N ILE* 1.3 55.4 + - - +
60N ASN* 2.7 30.2 + - - +
61N SER* 3.0 12.6 + - - -
99P GLY* 3.4 25.0 - - - -
100P PHE* 3.9 1.9 + - - -
101P GLY* 4.4 6.2 + - - -
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Residues in contact with ILE 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M PRO* 4.9 6.3 - - + -
83M LEU* 4.2 14.1 - - + -
102M ILE* 4.0 20.2 - - + -
103M ALA* 3.6 32.5 - - + +
54N LYS* 3.0 17.8 + - + +
55N ALA* 3.6 14.6 - - - +
57N SER* 1.3 72.0 - - - +
59N MET* 1.3 58.1 + - - +
61N SER* 3.1 5.2 + - - -
62N PHE* 2.9 27.1 + - + +
98P TYR* 3.6 40.4 - - + +
99P GLY* 3.6 13.1 - - - +
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Residues in contact with MET 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M THR* 3.8 28.0 - - + +
62M ILE* 3.6 38.6 - - + -
63M LEU* 4.0 13.9 - - + -
83M LEU* 3.8 26.7 - - + -
38N VAL* 4.4 15.0 - - + -
51N ILE* 4.3 11.2 - - + -
55N ALA 3.1 13.4 + - - +
56N MET* 3.1 12.7 + - - +
58N ILE* 1.3 80.3 - - - +
60N ASN* 1.3 56.4 + - - +
62N PHE* 3.5 11.7 + - + +
63N VAL* 3.0 36.1 + - + +
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Residues in contact with ASN 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N GLU 5.1 1.0 + - - -
33N SER* 3.4 26.0 - - - +
34N TYR* 3.1 42.9 + - + +
35N ALA* 5.6 0.9 - - + +
38N VAL* 5.6 1.3 - - - +
56N MET* 2.9 12.9 + - + +
57N SER* 2.7 16.8 + - - +
59N MET* 1.3 76.0 - - - +
61N SER* 1.3 53.8 + - - +
63N VAL* 3.4 3.7 + - - -
64N ASN* 2.5 49.6 + - - +
101P GLY* 6.0 0.6 - - - -
102P GLY* 4.6 6.7 + - - +
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Residues in contact with SER 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N SER* 3.0 7.3 + - - -
58N ILE 3.1 7.8 + - - -
60N ASN* 1.3 73.6 - - - +
62N PHE* 1.3 57.4 + - - +
64N ASN* 3.2 1.7 + - - +
65N ASP* 2.7 37.2 + - - +
97P LEU 4.8 2.2 + - - -
98P TYR* 3.7 18.7 - - - -
99P GLY* 3.1 28.0 + - - -
100P PHE 4.3 0.5 + - - -
101P GLY 3.9 10.9 + - - -
102P GLY 3.8 19.6 + - - -
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Residues in contact with PHE 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M LEU* 3.8 45.8 - - + -
59M THR* 4.1 3.8 - - - -
62M ILE* 3.8 29.4 - - + -
93M LEU* 5.2 4.0 - - + -
96M LEU* 4.2 12.3 - - + -
97M LEU* 3.9 29.2 - - + -
58N ILE* 2.9 11.2 + - + +
59N MET* 3.5 15.3 - - + +
61N SER* 1.3 77.3 - - - +
63N VAL* 1.3 75.8 + - + +
65N ASP* 3.7 0.9 - - - +
66N VAL* 3.0 55.3 + - + +
98P TYR* 3.5 18.5 - - + -
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Residues in contact with VAL 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M PHE* 3.9 10.8 - - + -
55M LEU* 4.3 14.2 - - + +
59M THR* 3.5 22.7 - - + +
34N TYR* 3.6 40.2 - - + -
38N VAL* 4.4 15.5 - - + -
59N MET* 3.0 18.4 + - + +
60N ASN* 3.9 4.5 - - - +
62N PHE* 1.3 87.8 - - + +
64N ASN* 1.3 56.7 + - - +
66N VAL* 3.3 3.9 + - - +
67N PHE* 2.9 29.5 + - - +
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Residues in contact with ASN 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M LEU* 5.9 1.2 - - - +
34N TYR* 3.9 17.9 - - - -
60N ASN* 2.5 49.5 + - - +
61N SER 3.6 4.0 - - - +
63N VAL* 1.3 76.8 - - - +
65N ASP* 1.3 61.9 + - - +
67N PHE* 3.4 7.6 + - - +
68N GLU* 3.0 31.6 + - - +
102P GLY* 3.1 33.8 + - - +
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Residues in contact with ASP 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M LEU* 4.9 0.2 - - - +
100M VAL* 4.2 2.0 - - - +
61N SER 2.7 17.5 + - - +
62N PHE 3.7 0.9 - - - +
64N ASN* 1.3 72.8 - - - +
66N VAL* 1.3 55.3 + - - +
68N GLU* 3.1 11.9 + - - +
69N ARG* 2.7 70.0 + - - +
91P LYS* 4.8 14.1 - - - +
96P THR* 4.8 9.0 + - + +
98P TYR* 2.6 36.6 + - + +
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Residues in contact with VAL 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU* 3.8 17.7 - - + -
58M LEU* 3.8 24.7 - - + -
96M LEU* 4.5 12.1 - - + -
97M LEU* 5.5 0.7 - - + -
62N PHE* 3.0 49.0 + - + +
63N VAL* 3.9 4.0 - - - +
65N ASP* 1.3 78.4 - - - +
67N PHE* 1.3 67.6 + - - +
68N GLU 3.0 1.3 - - - -
69N ARG* 4.0 11.3 - - - +
70N ILE* 3.0 33.6 + - + +
98N LEU* 5.1 4.0 - - + -
98P TYR* 4.9 0.2 - - - +
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Residues in contact with PHE 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 4.0 21.8 - - + -
33M LEU* 4.0 27.4 - - + -
34M LEU* 3.8 22.4 - - + -
39M TYR* 3.8 27.1 - + - -
51M LEU* 3.6 27.2 - - + +
55M LEU* 3.8 26.7 - - + +
34N TYR* 4.4 11.9 - - - +
63N VAL 2.9 18.5 + - - +
64N ASN* 3.5 9.2 - - - +
66N VAL* 1.3 76.0 - - - +
68N GLU* 1.3 60.3 + - + +
70N ILE* 3.6 3.8 - - - +
71N ALA* 2.8 39.5 + - + +
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Residues in contact with GLU 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 3.4 24.7 + - + +
64N ASN* 3.0 19.5 + - - +
65N ASP* 3.2 15.0 - - - +
67N PHE* 1.3 80.6 - - + +
69N ARG* 1.3 61.4 + - + +
70N ILE 3.2 1.3 - - - -
71N ALA* 4.0 0.6 - - - +
72N GLY* 2.8 30.3 + - - -
91P LYS* 4.1 24.4 + - - +
102P GLY* 5.6 1.2 - - - +
80R TYR* 6.1 1.4 - - - -
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Residues in contact with ARG 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M LEU* 2.9 54.5 + - - +
97M LEU* 4.4 1.8 - - - +
98M GLY 4.8 1.0 - - - +
99M ARG* 5.1 4.4 - - - +
100M VAL* 3.7 19.6 - - - +
65N ASP* 2.7 52.6 + - - +
66N VAL* 4.0 7.6 - - - +
68N GLU* 1.3 71.5 - - - +
70N ILE* 1.3 63.4 + - - +
72N GLY* 4.0 0.9 - - - -
73N GLU* 3.2 29.8 + - - +
76N ARG* 5.2 1.0 + - - -
98N LEU* 3.6 32.9 - - + +
98P TYR* 5.2 0.4 - - - -
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Residues in contact with ILE 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 3.7 31.0 - - + -
54M VAL* 4.0 24.5 - - + -
55M LEU* 4.7 0.4 - - + -
58M LEU* 5.0 1.6 - - + -
66N VAL* 3.0 34.4 + - + +
67N PHE 3.6 2.0 - - - +
69N ARG* 1.3 74.4 - - - +
71N ALA* 1.3 68.4 + - - +
73N GLU* 3.0 8.6 + - - +
74N ALA* 3.0 19.8 + - - +
91N ILE* 4.4 18.8 - - + +
94N ALA* 3.6 23.3 - - + +
95N VAL* 4.3 8.1 - - + -
98N LEU* 3.9 18.4 - - + -
99N LEU* 5.1 2.9 - - + -
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Residues in contact with ALA 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LEU* 4.4 12.6 - - + -
39M TYR* 3.5 41.0 - - + +
51M LEU* 5.1 2.0 - - + -
67N PHE* 2.8 30.4 + - + +
68N GLU 4.0 0.7 - - - +
70N ILE* 1.3 76.1 - - - +
72N GLY* 1.3 52.3 + - - +
74N ALA* 3.3 7.4 + - - +
75N SER* 2.8 34.3 + - - -
86N ILE* 4.6 1.4 - - - +
91N ILE* 5.6 1.3 - - - -
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Residues in contact with GLY 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 3.8 9.1 - - - -
68N GLU 2.8 18.3 + - - -
69N ARG* 4.0 0.9 - - - -
71N ALA* 1.3 78.0 - - - +
73N GLU* 1.3 59.6 + - - +
75N SER* 3.2 10.4 - - - -
76N ARG* 3.2 44.4 + - - -
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Residues in contact with GLU 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 3.7 15.1 + - - -
92L ARG* 2.6 49.3 + - - +
69N ARG 3.2 18.1 + - - +
70N ILE 3.0 10.1 + - - +
72N GLY* 1.3 74.9 - - - +
74N ALA* 1.3 57.8 + - - +
76N ARG* 3.3 25.1 + - - +
77N LEU* 3.1 31.7 + - - +
94N ALA* 3.8 21.8 - - + +
97N LEU* 3.8 10.2 - - + +
98N LEU* 4.7 7.2 - - + +
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Residues in contact with ALA 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N ILE 3.0 12.6 + - - +
71N ALA* 3.6 11.0 - - - +
73N GLU* 1.3 73.1 - - - +
75N SER* 1.3 66.1 + - - +
77N LEU* 3.3 12.9 + - - +
78N ALA* 3.1 22.0 + - - +
86N ILE* 4.2 12.7 - - + +
90N GLU* 4.1 24.3 - - + +
91N ILE* 4.5 10.3 - - + +
94N ALA* 3.8 10.0 - - + +
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Residues in contact with SER 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 2.8 36.6 + - - -
71N ALA 2.8 14.8 + - - -
72N GLY* 3.2 15.0 - - - -
74N ALA* 1.3 76.7 - - - +
76N ARG* 1.3 62.6 + - - +
78N ALA* 3.3 4.9 + - - +
79N HIS* 3.1 35.2 + - - -
86N ILE* 4.1 5.3 - - - +
38Q ASN* 5.4 1.2 + - - +
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Residues in contact with ARG 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 5.3 1.6 - - - +
91L LYS* 5.8 3.8 - - - -
92L ARG* 5.6 3.8 - - - +
69N ARG 5.2 1.2 + - - -
72N GLY* 3.2 30.9 + - - -
73N GLU* 3.3 50.7 + - - +
74N ALA 3.3 0.2 - - - -
75N SER* 1.3 77.6 - - - +
77N LEU* 1.3 60.9 + - - +
79N HIS* 3.2 6.0 + - - +
80N TYR* 2.8 71.9 + - + +
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Residues in contact with LEU 77 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 3.9 28.9 - - + -
75L HIS* 3.8 31.1 + - + +
73N GLU 3.1 21.2 + - - +
74N ALA* 3.3 12.1 + - - +
76N ARG* 1.3 75.7 - - - +
78N ALA* 1.3 62.2 + - - +
80N TYR* 4.1 5.3 - - - +
81N ASN* 2.7 34.0 + - - +
83N ARG* 5.2 0.2 - - - +
90N GLU* 3.7 19.1 - - + +
93N THR* 3.7 17.7 - - + +
94N ALA* 3.6 30.3 - - - +
97N LEU* 4.2 4.0 - - + -
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Residues in contact with ALA 78 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M ALA* 5.0 6.3 - - + -
74N ALA 3.1 11.9 + - - +
75N SER* 3.4 10.8 - - - +
76N ARG 3.2 0.2 - - - -
77N LEU* 1.3 77.4 - - - +
79N HIS* 1.3 63.7 + - + +
81N ASN 3.0 9.2 + - - -
83N ARG* 2.8 55.8 + - + +
85N THR 4.9 4.3 - - - +
86N ILE* 4.7 13.7 - - + -
90N GLU* 4.6 5.5 - - + +
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Residues in contact with HIS 79 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR 4.3 6.2 + - - -
40M ALA* 5.7 0.9 - - + -
75N SER* 3.1 26.7 + - - +
76N ARG* 3.2 9.4 + - + +
78N ALA* 1.3 85.4 - - + +
80N TYR* 1.3 67.9 + - + +
82N LYS* 3.3 14.2 + - - +
83N ARG 4.5 6.3 - - - +
36Q LYS* 3.3 14.2 + - - +
37Q GLY* 3.1 46.1 + - - -
38Q ASN* 2.9 20.2 + - - +
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Residues in contact with TYR 80 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 3.8 30.1 + + + -
88L TYR* 3.2 73.6 + + + +
91L LYS* 4.2 17.9 + - - +
76N ARG* 2.8 59.6 + - + +
77N LEU* 4.1 4.0 - - - +
79N HIS* 1.3 82.9 - - + +
81N ASN* 1.3 66.3 + - - +
82N LYS* 3.3 16.9 + - - -
68R GLU* 6.5 1.1 - - - -
----------------------------------------------------------
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Residues in contact with ASN 81 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 5.1 3.5 + - - +
75L HIS* 3.3 30.5 + - + +
76L ALA* 3.2 28.4 - - - +
78L ARG* 5.2 0.9 + - - -
77N LEU* 2.7 30.1 + - - +
78N ALA 3.0 3.7 + - - +
80N TYR* 1.3 81.5 - - - +
82N LYS* 1.3 71.0 + - - +
83N ARG* 2.9 33.3 + - + +
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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