Contacts of the helix formed by residues 46 - 73 (chain M) in PDB entry 5OXV
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 GLY 46 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-197J G 4.9 0.2 + - - -
44M GLY* 3.5 0.4 - - - -
45M ALA* 1.3 79.6 - - - +
47M ALA* 1.3 52.7 + - - +
49M VAL* 2.9 11.1 + - - +
50M TYR* 2.6 33.1 + - - +
88N SER* 3.8 17.2 - - - +
115N VAL* 3.8 13.3 - - - +
118N TYR* 5.3 4.7 - - - -
119N THR* 6.5 0.4 - - - -
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Residues in contact with ALA 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LEU* 4.5 6.7 - - + -
43M VAL* 5.1 1.3 - - + -
44M GLY 4.0 2.6 + - - +
46M GLY* 1.3 72.4 - - - +
48M PRO* 1.3 65.9 - - + +
49M VAL 3.0 1.6 - - - -
50M TYR* 3.9 1.5 - - - +
51M LEU* 2.8 34.8 + - - +
86N ILE* 3.6 15.3 - - + +
87N THR* 3.6 5.4 - - - -
88N SER* 3.6 24.0 - - - +
91N ILE* 3.6 24.4 - - + +
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Residues in contact with PRO 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ARG* 4.9 4.7 - - - +
27M VAL* 3.7 14.7 - - + +
30M VAL* 3.7 16.0 - - + +
31M HIS* 3.4 48.5 - - + +
34M LEU* 4.0 5.8 - - + -
44M GLY 3.2 18.6 - - - +
45M ALA* 3.4 15.5 - - - +
47M ALA* 1.3 91.8 - - + +
49M VAL* 1.3 58.9 + - + +
52M ALA* 3.0 29.5 + - - +
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Residues in contact with VAL 49 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ARG* 5.4 0.2 - - - -
21M ALA* 4.0 11.0 - - + -
23M LEU* 3.8 6.5 - - + +
27M VAL* 3.2 28.7 - - + -
45M ALA 4.1 11.7 - - - +
46M GLY* 2.9 9.3 + - - +
48M PRO* 1.3 77.0 - - + +
50M TYR* 1.3 69.3 + - - +
52M ALA* 3.4 1.9 + - - -
53M ALA* 3.1 22.7 + - - +
114N ALA* 3.6 31.9 - - + +
115N VAL* 3.8 9.2 - - + +
118N TYR* 3.9 28.0 - - + -
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Residues in contact with TYR 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M GLY 2.6 18.5 + - - +
47M ALA* 3.9 4.5 - - - +
49M VAL* 1.3 74.0 - - - +
51M LEU* 1.3 62.0 + - - +
53M ALA* 3.2 4.3 - - - +
54M VAL* 2.9 41.0 + - + +
88N SER* 3.4 32.1 - - - -
91N ILE* 3.7 11.9 - - + -
92N GLN* 2.7 62.2 + - + +
95N VAL* 4.5 4.7 - - + -
107N ALA 4.4 2.9 - - - -
108N VAL* 3.3 18.7 - - - +
111N GLY* 3.7 28.0 - - - -
112N THR* 4.0 4.3 - - + -
115N VAL* 3.6 17.9 - - + +
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Residues in contact with LEU 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL* 4.2 6.1 - - + -
34M LEU* 4.1 20.2 - - + -
47M ALA 2.8 21.2 + - - +
48M PRO 4.6 0.4 - - - +
50M TYR* 1.3 69.8 - - - +
52M ALA* 1.3 64.1 + - - +
53M ALA 2.8 5.0 + - - -
54M VAL* 2.8 7.2 + - + -
55M LEU* 2.8 45.5 + - + +
67N PHE* 4.1 35.0 - - + +
70N ILE* 3.9 35.9 - - + -
71N ALA* 5.2 1.6 - - + -
91N ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LEU* 4.4 8.3 - - + -
25M PHE* 3.5 29.7 - - + +
27M VAL* 4.5 4.7 - - - -
30M VAL* 4.0 21.4 - - + +
48M PRO 3.0 23.1 + - - +
49M VAL 4.0 2.5 - - - +
51M LEU* 1.3 76.1 - - - +
53M ALA* 1.3 52.5 + - - +
55M LEU* 3.6 7.6 - - - +
56M GLU* 2.8 33.4 + - - +
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Residues in contact with ALA 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LEU* 3.5 25.0 - - + +
49M VAL 3.1 12.8 + - - +
50M TYR 3.2 12.8 - - - +
51M LEU 2.9 0.4 - - - -
52M ALA* 1.3 75.1 - - - +
54M VAL* 1.3 54.8 + - - +
56M GLU* 3.1 2.3 + - - +
57M TYR* 2.5 36.1 + - - +
110N GLU* 3.7 30.7 - - + +
111N GLY* 4.2 0.7 - - - -
114N ALA* 4.0 5.6 - - + -
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Residues in contact with VAL 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 2.9 45.3 - - + +
51M LEU* 2.8 12.1 + - + +
53M ALA* 1.3 72.4 - - - +
55M LEU* 1.3 64.9 + - - +
57M TYR* 3.6 6.0 - - - +
58M LEU* 3.1 38.0 + - + +
70N ILE* 4.4 6.7 - - + -
95N VAL* 4.1 19.3 - - + -
99N LEU* 4.4 2.2 - - + -
107N ALA* 3.6 34.8 - - + +
111N GLY* 4.5 1.3 - - - -
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Residues in contact with LEU 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M PHE* 4.0 11.4 - - + -
30M VAL* 4.8 6.3 - - + -
51M LEU* 2.8 43.3 + - + +
52M ALA* 3.6 9.2 - - - +
54M VAL* 1.3 78.0 - - - +
56M GLU* 1.3 53.8 + - - +
58M LEU* 3.9 4.6 - - + +
59M THR* 2.6 36.8 + - - +
34N TYR* 4.8 2.5 - - + +
62N PHE* 5.4 2.6 - - + -
63N VAL* 3.5 41.7 - - + +
66N VAL* 4.2 14.4 - - + -
67N PHE* 3.8 29.2 - - + +
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Residues in contact with GLU 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M GLY 5.1 1.4 - - - +
23M LEU* 3.0 25.0 - - + +
24M GLN* 2.6 45.9 + - - +
25M PHE* 3.5 16.0 + - + -
52M ALA 2.8 23.1 + - - +
53M ALA* 3.4 6.7 - - - +
55M LEU* 1.3 69.4 - - - +
57M TYR* 1.3 68.8 + - - +
59M THR* 3.2 9.2 - - - +
60M ALA* 3.1 21.1 + - - +
41N VAL* 3.6 23.7 - - + +
44N GLN* 3.8 9.2 + - - +
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Residues in contact with TYR 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ALA 2.5 19.7 + - - +
54M VAL* 3.6 5.6 - - - +
55M LEU 3.3 0.2 - - - -
56M GLU* 1.3 75.1 - - - +
58M LEU* 1.3 67.8 + - + +
60M ALA* 3.0 25.5 + - + +
61M GLU* 3.0 34.4 + - + -
103N LEU* 3.4 40.1 - - + +
106N HIS* 3.0 40.1 + + + +
107N ALA* 3.6 20.2 - - + -
110N GLU* 3.8 37.2 - - + -
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Residues in contact with LEU 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M VAL* 3.1 32.7 + - + +
55M LEU* 4.0 3.8 - - + +
57M TYR* 1.3 87.7 - - + +
59M THR* 1.3 65.3 + - - +
60M ALA 3.1 1.6 - - - -
61M GLU* 3.2 6.8 + - - +
62M ILE* 3.2 26.5 + - - +
93M LEU* 5.1 3.7 - - + +
96M LEU* 4.5 5.6 - - + -
62N PHE* 4.1 17.0 - - + -
66N VAL* 3.9 28.5 - - + -
70N ILE* 5.1 0.4 - - + -
99N LEU* 4.3 22.0 - - + -
103N LEU* 3.6 37.0 - - + -
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Residues in contact with THR 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M PHE* 3.3 34.5 - - + -
55M LEU 2.6 28.8 + - - +
56M GLU* 3.2 13.5 - - + +
58M LEU* 1.3 74.1 - - - +
60M ALA* 1.3 56.0 + - - +
62M ILE* 3.9 1.3 - - - +
63M LEU* 3.0 47.2 + - - +
38N VAL* 4.5 3.8 - - - +
41N VAL* 4.3 2.6 - - + +
59N MET* 3.4 20.7 - - - +
62N PHE* 4.2 9.5 - - - -
63N VAL* 4.9 7.0 - - + -
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Residues in contact with ALA 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M GLU* 3.1 11.6 + - - +
57M TYR* 3.0 19.0 + - + +
59M THR* 1.3 75.4 - - - +
61M GLU* 1.3 53.0 + - - +
63M LEU* 3.1 2.6 + - - +
64M GLU* 2.6 37.8 + - - +
41N VAL* 3.9 19.9 - - + +
45N VAL* 4.3 16.8 - - + +
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Residues in contact with GLU 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 3.0 42.5 + - + +
58M LEU* 3.2 11.8 + - - +
60M ALA* 1.3 77.1 - - - +
62M ILE* 1.3 61.2 + - - +
64M GLU* 3.3 11.0 - - + +
65M LEU* 3.2 39.9 + - + +
90M ASP* 4.9 4.0 - - - +
93M LEU* 4.8 10.3 - - + -
103N LEU* 4.1 17.2 - - + +
106N HIS* 5.3 3.8 + - - -
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Residues in contact with ILE 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M LEU 3.2 16.6 + - - +
59M THR 3.9 3.8 - - - +
60M ALA 3.2 0.6 - - - -
61M GLU* 1.3 75.2 - - - +
63M LEU* 1.3 62.1 + - - +
65M LEU* 3.2 2.4 + - - +
66M ALA* 2.9 33.2 + - + +
83M LEU* 3.6 28.0 - - + -
86M ALA* 4.5 2.7 - - + +
87M VAL* 4.1 20.0 - - + -
93M LEU* 3.6 35.9 - - + -
97M LEU* 4.8 3.6 - - + -
59N MET* 3.8 14.4 - - + -
62N PHE* 4.0 31.6 - - + -
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Residues in contact with LEU 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M THR* 3.0 38.4 + - - +
60M ALA 3.7 2.7 - - - +
62M ILE* 1.3 75.4 - - - +
64M GLU* 1.3 70.2 + - - +
66M ALA* 4.1 3.5 - - - +
67M GLY* 3.0 18.5 + - - -
78M ILE* 4.5 8.0 - - + +
83M LEU* 5.6 1.6 - - + -
38N VAL* 3.6 34.3 - - + +
41N VAL* 3.7 14.4 - - + -
42N LEU* 3.9 26.1 - - + +
45N VAL* 4.1 13.5 - - + -
46N HIS* 4.5 2.9 + - - -
51N ILE* 4.4 13.2 - - + -
59N MET* 3.9 20.2 - - + -
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Residues in contact with GLU 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M ALA 2.6 21.7 + - - +
61M GLU* 3.3 16.0 - - + +
63M LEU* 1.3 76.8 - - - +
65M LEU* 1.3 74.5 + - + +
68M ASN* 3.0 35.4 + - - +
45N VAL* 4.1 17.4 - - + +
46N HIS* 3.4 22.2 + - - -
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Residues in contact with LEU 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLU* 3.2 25.1 + - + +
62M ILE 3.2 2.6 + - - +
64M GLU* 1.3 87.5 - - + +
66M ALA* 1.3 60.2 + - - +
68M ASN* 3.4 17.1 - - + +
69M ALA* 3.1 25.3 + - - +
86M ALA* 3.6 19.8 - - + +
90M ASP* 3.7 31.4 - - + +
93M LEU* 4.0 12.6 - - + -
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Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ILE 2.9 17.7 + - - +
63M LEU* 4.1 2.5 - - - +
65M LEU* 1.3 74.5 - - - +
67M GLY* 1.3 53.6 + - - +
69M ALA* 2.8 7.4 + - - +
70M ALA* 2.7 33.3 + - - +
78M ILE* 4.2 12.3 - - + -
82M HIS* 3.6 29.7 - - - +
83M LEU* 3.7 24.2 - - + -
86M ALA* 3.4 3.9 - - + +
----------------------------------------------------------
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Residues in contact with GLY 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LEU 3.0 15.9 + - - -
64M GLU 3.6 3.6 - - - -
66M ALA* 1.3 70.9 - - - +
68M ASN* 1.3 65.7 + - - +
70M ALA* 2.8 9.7 + - - +
71M ARG* 2.8 23.4 + - - +
78M ILE* 4.0 15.0 - - - +
46N HIS* 3.5 19.9 - - - -
49N THR* 4.7 4.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M GLU* 3.0 21.9 + - - +
65M LEU* 3.4 24.3 - - + +
67M GLY* 1.3 70.2 - - - +
69M ALA* 1.3 51.8 + - - +
71M ARG* 2.8 18.0 + - - +
72M ASP* 2.8 45.1 + - - +
46N HIS* 3.1 20.4 + - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M LEU 3.1 10.9 + - - +
66M ALA 2.8 17.2 + - - +
68M ASN* 1.3 76.9 - - - +
70M ALA* 1.3 54.4 + - - +
72M ASP* 3.4 11.1 + - - -
73M ASN* 2.6 40.3 + - - +
82M HIS* 4.0 22.9 - - + +
85M LEU* 4.5 13.5 - - + -
86M ALA* 4.8 2.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ALA 2.7 13.5 + - - +
67M GLY* 2.8 13.6 + - - +
69M ALA* 1.3 69.1 - - - +
71M ARG* 1.3 54.1 + - - +
73M ASN 3.3 0.9 - - - -
74M LYS 2.8 12.0 + - - -
75M LYS* 2.7 42.8 + - - +
77M ARG 4.4 4.7 - - - +
78M ILE* 4.3 10.5 - - + -
82M HIS* 3.6 33.1 - - + +
49N THR* 4.9 3.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M GLY 2.8 10.8 + - - +
68M ASN* 3.1 14.0 + - - +
70M ALA* 1.3 75.3 - - - +
72M ASP* 1.3 58.8 + - - +
74M LYS* 2.7 32.1 + - - +
75M LYS 4.0 4.7 + - - +
45N VAL 5.3 0.2 + - - -
46N HIS* 3.6 48.1 + - + +
47N PRO* 5.4 2.4 - - - +
48N ASP* 5.6 5.3 + - - +
49N THR* 4.5 10.8 + - + -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ASN* 2.8 34.2 + - - +
69M ALA* 3.5 12.2 + - - +
71M ARG* 1.3 74.4 - - - +
73M ASN* 1.3 63.2 + - - +
74M LYS* 3.2 11.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M ALA* 2.6 32.3 + - - +
70M ALA 3.3 2.5 - - - +
72M ASP* 1.3 79.6 - - - +
74M LYS* 1.3 69.2 + - - +
75M LYS* 3.6 14.1 + - - +
81M ARG* 5.2 4.6 - - - +
82M HIS* 3.9 19.4 - - - +
85M LEU* 3.7 28.6 - - - +
----------------------------------------------------------
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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