Contacts of the helix formed by residues 55 - 84 (chain N) in PDB entry 5GSE
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 55 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J A 3.6 19.3 - - - -
77M ARG* 4.4 6.7 - - - +
78M ILE 3.1 15.3 + - - -
79M ILE* 3.3 28.8 - - - +
80M PRO* 3.7 2.3 - - - +
54N ILE* 1.3 80.2 - - - +
56N SER* 1.3 66.0 + - - +
57N LYS* 4.3 3.1 + - - -
58N ALA* 3.5 12.1 + - - +
59N MET* 3.0 20.0 + - - +
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Residues in contact with SER 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J G 4.5 2.0 - - - -
20J A 2.2 39.6 + - - -
55N SER* 1.3 74.4 - - - +
57N LYS* 1.3 66.6 + - - +
59N MET* 3.0 11.1 + - - +
60N GLY* 2.9 18.0 + - - -
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Residues in contact with LYS 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M PRO* 3.8 19.3 - - + -
103M ALA* 5.2 6.5 - - - +
104M GLN* 4.8 19.5 - - + +
55N SER* 3.4 3.2 + - - +
56N SER* 1.3 78.1 - - - +
58N ALA* 1.3 58.5 + - - +
60N GLY* 2.8 19.0 + - - +
61N ILE* 2.9 19.1 + - + +
99P GLY* 3.5 26.8 + - - +
100P PHE* 4.0 26.1 - - - -
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Residues in contact with ALA 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ILE* 3.4 27.1 - - + +
79M ILE 4.0 0.7 - - - -
80M PRO* 3.7 16.5 - - + +
83M LEU* 3.8 10.4 - - + +
54N ILE* 3.6 14.8 - - + -
55N SER* 3.4 7.9 + - - +
56N SER 3.4 0.4 - - - -
57N LYS* 1.3 76.3 - - - +
59N MET* 1.3 57.9 + - - +
61N ILE* 3.3 14.8 + - - +
62N MET* 3.0 32.4 + - - +
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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
----------------------------------------------------------
38N SER* 3.5 39.5 - - - +
41N VAL* 3.3 34.3 - - + -
42N TYR* 4.8 8.1 - - + -
54N ILE* 3.5 36.7 - - + +
55N SER 3.0 12.2 + - - +
56N SER* 3.0 16.8 + - - +
58N ALA* 1.3 77.5 - - - +
60N GLY* 1.3 54.8 + - - +
62N MET* 3.3 3.2 + - - +
63N ASN* 2.9 28.4 + - + +
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Residues in contact with GLY 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N SER 2.9 9.3 + - - -
57N LYS* 2.8 8.5 + - - -
59N MET* 1.3 74.6 - - - +
61N ILE* 1.3 57.7 + - - +
63N ASN* 3.8 5.8 - - - +
64N SER* 2.9 34.5 + - - -
99P GLY* 3.8 17.0 - - - -
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Residues in contact with ILE 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M PRO* 3.5 43.7 - - + -
83M LEU* 3.7 16.2 - - + -
102M ILE* 3.6 41.7 - - + -
103M ALA* 3.7 6.3 - - + +
57N LYS* 2.9 16.8 + - + +
58N ALA* 3.3 8.7 + - - +
60N GLY* 1.3 77.0 - - - +
62N MET* 1.3 58.4 + - - +
64N SER* 3.4 1.9 + - - -
65N PHE* 2.9 29.2 + - + +
98P TYR* 3.9 17.6 - - + +
99P GLY* 4.3 11.2 - - - -
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Residues in contact with MET 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M THR* 3.7 39.7 - - + +
62M ILE* 4.3 12.1 - - + -
63M LEU* 3.9 19.5 - - + -
83M LEU* 3.8 28.0 - - + -
41N VAL* 4.3 19.5 - - + -
54N ILE* 4.3 14.4 - - + -
58N ALA 3.0 17.2 + - - +
59N MET 3.3 8.7 + - - +
61N ILE* 1.3 77.9 - - - +
63N ASN* 1.3 57.2 + - - +
65N PHE* 3.2 19.0 + - + +
66N VAL* 3.0 34.1 + - - +
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Residues in contact with ASN 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N SER* 3.3 18.2 + - - +
37N TYR* 2.4 50.6 + - - +
38N SER* 3.5 4.6 + - - +
41N VAL* 5.7 0.9 - - - +
59N MET* 2.9 17.7 + - + +
60N GLY* 3.8 7.0 - - - +
62N MET* 1.3 75.8 - - - +
64N SER* 1.3 59.1 + - - +
66N VAL* 3.3 5.7 + - - +
67N ASN* 3.0 60.5 + - - +
101P GLY 5.7 2.8 + - - -
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Residues in contact with SER 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N GLY 2.9 19.8 + - - -
61N ILE 3.7 0.4 - - - -
63N ASN* 1.3 76.5 - - - +
65N PHE* 1.3 57.1 + - - +
67N ASN* 3.9 6.9 - - - +
68N ASP* 2.9 31.7 + - - +
97P LEU 4.5 3.4 + - - -
98P TYR* 3.5 32.6 - - - -
99P GLY* 3.2 12.3 + - - -
100P PHE 4.1 12.1 + - - -
101P GLY 4.9 2.8 + - - -
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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
----------------------------------------------------------
55M LEU* 4.9 2.5 - - + -
58M LEU* 3.5 28.5 - - + -
59M THR* 3.9 25.6 - - - -
62M ILE* 3.4 35.4 - - + -
96M LEU* 4.5 7.2 - - + -
97M LEU* 4.1 19.7 - - + -
61N ILE* 2.9 15.0 + - + +
62N MET* 3.4 18.2 - - + +
63N ASN 3.2 0.2 - - - -
64N SER* 1.3 76.6 - - - +
66N VAL* 1.3 76.7 + - + +
68N ASP 3.3 0.2 + - - -
69N ILE* 2.9 56.3 + - + +
98P TYR* 3.6 15.9 - - + -
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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
----------------------------------------------------------
25M PHE* 3.8 18.2 - - + -
55M LEU* 3.9 17.3 - - + +
59M THR* 3.5 24.5 - - - +
37N TYR* 3.6 42.4 - - + -
41N VAL* 4.5 8.3 - - + -
62N MET* 3.0 21.6 + - + +
63N ASN 3.3 4.5 + - - +
65N PHE* 1.3 82.6 - - + +
67N ASN* 1.3 59.8 + - - +
70N PHE* 2.9 30.7 + - - +
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Residues in contact with ASN 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M LEU* 5.4 2.4 - - - +
37N TYR* 3.3 23.1 + - - -
63N ASN* 3.0 40.4 + - - +
64N SER* 3.9 6.5 - - - +
66N VAL* 1.3 77.4 - - - +
68N ASP* 1.3 63.4 + - - +
70N PHE* 3.3 9.6 + - - +
71N GLU* 2.9 24.3 + - - +
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Residues in contact with ASP 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M VAL* 4.4 4.2 - - - +
64N SER 2.9 15.6 + - - +
65N PHE 3.7 0.9 - - - +
67N ASN* 1.3 76.3 - - - +
69N ILE* 1.3 64.7 + - - +
71N GLU* 3.0 9.0 + - - +
72N ARG* 2.7 56.9 + - - +
91P LYS* 5.7 4.1 - - - +
96P THR* 4.4 10.8 + - - +
98P TYR* 2.3 41.6 + - + +
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Residues in contact with ILE 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LEU* 3.5 22.4 - - + -
58M LEU* 4.0 22.7 - - + -
96M LEU* 4.7 7.0 - - + -
97M LEU* 4.2 6.3 - - + -
65N PHE* 2.9 51.4 + - + +
66N VAL* 5.1 0.2 - - - -
68N ASP* 1.3 90.6 - - - +
70N PHE* 1.3 64.0 + - - +
72N ARG* 3.3 23.8 + - + +
73N ILE* 2.9 39.8 + - + +
102N LEU* 5.4 2.5 - - + -
98P TYR* 3.9 1.6 - - - +
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Residues in contact with PHE 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 3.5 27.8 - - + -
33M LEU* 3.6 33.0 - - + -
34M LEU* 3.7 20.6 - - + -
39M TYR* 3.9 20.4 - + - -
51M LEU* 3.7 27.0 - - + +
55M LEU* 3.9 18.1 - - + +
37N TYR* 4.7 10.3 - - - +
66N VAL 2.9 20.7 + - - +
67N ASN* 3.4 9.9 - - - +
69N ILE* 1.3 78.6 - - - +
71N GLU* 1.3 62.9 + - + +
73N ILE* 3.8 0.7 - - - +
74N ALA* 2.9 35.2 + - + +
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Residues in contact with GLU 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 4.0 20.4 - - + +
67N ASN 2.9 14.5 + - - +
68N ASP* 3.0 9.2 + - - +
70N PHE* 1.3 84.1 - - + +
72N ARG* 1.3 58.5 + - + +
74N ALA* 4.7 0.2 - - - -
75N GLY* 2.9 25.7 + - - -
88P TYR* 5.9 1.9 - - - -
91P LYS* 3.1 33.3 + - - +
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Residues in contact with ARG 72 (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 51.7 + - - +
97M LEU* 4.8 0.4 - - - +
100M VAL* 4.8 7.3 - - - +
68N ASP* 2.7 55.7 + - - +
69N ILE* 3.7 16.9 - - + +
71N GLU* 1.3 77.9 - - + +
73N ILE* 1.3 64.4 + - + +
75N GLY* 3.7 0.3 - - - -
76N GLU* 2.9 21.3 + - - +
79N ARG* 5.1 1.4 + - - -
101N LEU* 3.4 34.1 + - + +
96P THR* 5.6 2.0 + - - +
98P TYR* 4.5 0.2 + - - -
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Residues in contact with ILE 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU* 4.3 23.1 - - + -
54M VAL* 3.6 29.4 - - + -
58M LEU* 5.6 0.2 - - + -
69N ILE* 2.9 35.8 + - + +
70N PHE 3.9 2.2 - - - +
72N ARG* 1.3 75.8 - - + +
74N ALA* 1.3 58.4 + - - +
77N ALA* 2.9 30.5 + - - +
94N ILE* 4.3 17.7 - - + +
97N ALA* 3.8 7.3 - - + +
98N VAL* 3.6 25.8 - - + -
101N LEU* 3.5 20.2 - - + -
102N LEU* 5.0 9.0 - - + -
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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
----------------------------------------------------------
34M LEU* 3.8 25.8 - - + -
39M TYR* 3.4 39.0 - - + +
51M LEU* 4.8 4.0 - - + +
70N PHE* 2.9 20.7 + - + +
71N GLU 4.3 0.2 - - - +
73N ILE* 1.3 75.3 - - - +
75N GLY* 1.3 59.9 + - - +
77N ALA* 3.4 6.9 + - - +
78N SER* 2.9 24.4 + - - -
89N ILE* 4.7 0.8 - - - +
94N ILE* 6.1 0.9 - - - -
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Residues in contact with GLY 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR* 3.9 10.6 - - - -
71N GLU* 2.9 20.3 + - - -
72N ARG 3.7 0.7 - - - -
74N ALA* 1.3 76.1 - - - +
76N GLU* 1.3 61.7 + - - +
78N SER* 3.1 5.3 + - - -
79N ARG* 3.0 36.0 + - - +
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 2.5 31.1 + - - -
92L ARG* 3.2 21.9 + - - +
72N ARG 2.9 16.7 + - - +
75N GLY* 1.3 74.7 - - - +
77N ALA* 1.3 57.6 + - - +
79N ARG* 3.1 35.5 + - - +
80N LEU* 2.9 35.7 + - + +
97N ALA* 3.7 20.2 - - + +
100N LEU* 3.4 25.9 - - + +
101N LEU* 4.3 10.2 - - + +
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Residues in contact with ALA 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N ILE 2.9 19.5 + - - +
74N ALA* 3.6 7.6 - - - +
76N GLU* 1.3 77.7 - - - +
78N SER* 1.3 56.7 + - - +
80N LEU* 3.4 3.1 + - - +
81N ALA* 2.9 29.3 + - - +
89N ILE* 4.2 9.5 - - + +
93N GLU* 3.9 22.0 - - + +
94N ILE* 4.1 26.0 - - + -
97N ALA* 3.8 6.8 - - + +
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Residues in contact with SER 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ASN 5.0 0.3 + - - -
39M TYR* 2.5 45.3 + - - +
74N ALA 2.9 17.6 + - - -
75N GLY* 3.6 4.3 - - - -
77N ALA* 1.3 74.4 - - - +
79N ARG* 1.3 62.0 + - - +
81N ALA* 3.3 4.4 + - - +
82N HIS* 3.0 27.4 + - - +
89N ILE* 4.0 7.3 - - - +
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Residues in contact with ARG 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 4.5 2.8 + - - -
88L TYR* 5.1 11.0 - - + -
92L ARG* 5.4 3.2 - - - +
72N ARG 5.1 1.0 + - - -
75N GLY* 3.0 14.8 + - - +
76N GLU* 3.1 59.5 + - - +
78N SER* 1.3 79.6 - - - +
80N LEU* 1.3 57.5 + - - +
82N HIS* 3.1 8.4 + - + +
83N TYR* 2.9 29.6 + - - +
101N LEU* 5.9 1.0 - - - +
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Residues in contact with LEU 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L THR 5.3 0.4 - - - +
72L TYR* 3.5 36.1 - - + -
75L HIS* 3.4 33.8 + - + +
88L TYR* 6.5 0.2 - - - -
76N GLU* 2.9 23.3 + - - +
77N ALA* 3.8 2.2 - - - +
79N ARG* 1.3 74.6 - - - +
81N ALA* 1.3 62.6 + - - +
83N TYR* 4.1 4.4 + - + +
84N ASN* 2.8 35.2 + - - +
93N GLU* 3.7 16.8 - - + +
96N THR* 3.2 29.4 - - - +
97N ALA* 3.8 13.0 - - - +
100N LEU* 4.6 7.0 - - + -
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Residues in contact with ALA 81 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M TYR 5.9 0.4 - - - +
40M SER* 5.8 1.6 - - - -
77N ALA 2.9 17.6 + - - +
78N SER* 3.6 5.6 - - - +
79N ARG 3.3 0.2 - - - -
80N LEU* 1.3 76.5 - - - +
82N HIS* 1.3 62.4 + - - +
84N ASN* 3.4 4.5 + - - +
85N LYS 3.2 2.9 + - - -
86N ARG* 3.1 42.8 + - - +
87N SER 5.6 0.2 - - - -
88N THR 4.1 17.5 - - - +
89N ILE* 4.4 9.6 - - + -
93N GLU* 4.1 12.7 - - + +
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Residues in contact with HIS 82 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L TYR* 5.6 2.4 + - - -
78N SER* 3.0 14.3 + - - +
79N ARG* 3.1 11.4 + - - +
81N ALA* 1.3 73.2 - - - +
83N TYR* 1.3 69.4 + - - +
84N ASN 3.0 2.0 - - - -
85N LYS* 2.9 24.4 + - - +
86N ARG 4.9 1.3 - - - -
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Residues in contact with TYR 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR* 4.6 15.0 - + + -
78L ARG* 3.2 20.6 + - - -
82L THR* 3.3 14.2 - - - +
84L MET* 3.5 27.1 - - + +
85L ASP* 2.8 27.1 + - - -
88L TYR* 3.2 50.5 - + + -
79N ARG 2.9 13.7 + - - +
80N LEU* 4.4 5.6 - - - +
82N HIS* 1.3 79.2 + - - +
84N ASN* 1.3 90.7 + - - +
85N LYS* 3.6 11.1 + - - +
----------------------------------------------------------
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Residues in contact with ASN 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR 5.4 0.8 + - - -
75L HIS* 3.2 26.8 - - - +
76L ALA* 3.5 21.6 - - - +
78L ARG* 4.8 0.2 + - - -
80N LEU* 2.8 26.3 + - - +
81N ALA* 3.4 4.1 + - - +
82N HIS 3.0 1.0 - - - -
83N TYR* 1.3 102.1 - - - +
85N LYS* 1.3 62.6 + - - +
86N ARG* 2.9 37.3 + - + +
93N GLU* 5.8 0.2 - - - +
----------------------------------------------------------
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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).
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