Contacts of the helix formed by residues 48 - 72 (chain N) in PDB entry 3SDI
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 48 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H HIS* 5.8 0.5 - - - +
47N GLY* 1.3 68.1 - - - -
49N ALA* 1.3 59.9 + - - +
50N ALA* 3.5 8.1 + - - +
51N ASP* 3.2 29.7 + - - +
52N THR* 2.9 32.3 + - - +
96N THR* 3.0 26.7 + - - +
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Residues in contact with ALA 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H SER* 3.7 19.7 - - - +
20N THR* 5.8 9.2 - - + -
45N ARG* 4.6 4.5 - - - +
47N GLY 3.3 6.8 + - - -
48N SER* 1.3 69.4 + - - +
50N ALA* 1.3 64.4 + - - +
52N THR* 3.2 7.6 + - - -
53N GLN* 3.0 38.1 + - - +
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Residues in contact with ALA 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H PHE* 3.7 8.5 - - + -
116H HIS* 3.2 45.5 - - + +
117H GLY 4.1 2.9 - - - +
118H SER* 3.5 19.7 - - - +
48N SER* 3.3 7.9 + - - +
49N ALA* 1.3 77.2 - - - +
51N ASP* 1.3 65.4 + - - +
53N GLN* 3.9 1.6 - - - +
54N ALA* 3.0 25.5 + - - +
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Residues in contact with ASP 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H PHE* 3.5 22.4 - - - -
91H GLN* 5.0 3.8 + - - +
48N SER* 3.2 24.9 + - - +
50N ALA* 1.3 78.0 - - - +
52N THR* 1.3 57.2 + - - +
54N ALA* 3.4 1.7 + - - +
55N ILE* 2.9 35.8 + - - +
94N ASN 3.7 5.6 - - - +
95N LEU* 3.3 23.8 - - + +
96N THR* 2.9 35.5 + - - +
97N ALA* 4.6 3.4 - - + -
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Residues in contact with THR 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N ARG* 2.9 45.4 + - + +
46N SER 3.4 29.8 - - - +
48N SER 2.9 23.3 + - - +
49N ALA* 3.2 4.3 + - - -
51N ASP* 1.3 70.3 - - - +
53N GLN* 1.3 56.2 + - - +
55N ILE* 3.5 7.8 + - - +
56N ALA* 2.8 34.3 + - - +
97N ALA* 3.9 18.6 - - + -
99N ILE* 4.7 8.2 - - + +
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Residues in contact with GLN 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR* 3.4 40.3 + - + +
84H LYS* 2.9 21.2 + - - +
117H GLY 5.1 1.1 - - - +
118H SER* 3.3 10.6 - - - -
119H THR 2.9 43.5 + - - +
120H ASP* 5.2 0.8 + - - -
45N ARG* 3.7 18.1 - - - +
49N ALA* 3.0 24.2 + - - +
50N ALA 3.9 3.1 - - - +
52N THR* 1.3 74.2 + - - +
54N ALA* 1.3 59.7 + - - +
56N ALA* 3.1 1.3 + - - -
57N ASP* 2.8 37.4 + - - +
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Residues in contact with ALA 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TYR* 5.0 0.7 + - - -
84H LYS* 5.9 4.0 - - + +
88H PHE* 3.8 35.0 - - + -
117H GLY 5.8 0.9 + - - +
50N ALA 3.0 18.5 + - - +
51N ASP 3.7 3.8 - - - +
53N GLN* 1.3 76.0 - - - +
55N ILE* 1.3 61.9 + - + +
57N ASP* 3.8 8.8 - - - +
58N ILE* 3.2 34.5 + - + +
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Residues in contact with ILE 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N ASP 2.9 21.9 + - - +
52N THR* 3.7 4.5 - - - +
54N ALA* 1.3 75.4 - - + +
56N ALA* 1.3 66.7 + - - +
58N ILE* 3.1 6.3 + - + +
59N VAL* 3.0 21.5 + - - +
83N PHE* 3.6 31.0 - - + -
86N LEU* 4.1 24.9 - - + +
87N CYS* 4.1 10.8 - - - -
95N LEU* 3.6 34.3 - - + -
97N ALA* 3.8 24.5 - - + -
99N ILE* 3.9 5.6 - - + -
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Residues in contact with ALA 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR* 3.5 17.7 - - - +
35N THR* 4.1 19.5 - - + -
37N VAL* 3.8 7.7 - - + +
43N CYS* 4.8 4.9 - - - -
45N ARG* 4.3 9.0 - - + -
52N THR 2.8 22.5 + - - +
55N ILE* 1.3 76.7 - - - +
57N ASP* 1.3 56.4 + - - +
59N VAL* 3.2 2.3 + - - +
60N GLN* 3.0 31.0 + - - +
83N PHE* 4.4 9.9 - - + -
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Residues in contact with ASP 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR* 2.9 24.6 + - - -
2211 THR* 5.7 1.0 + - - -
101G TYR* 3.7 21.8 - - + -
81H GLN* 4.0 18.3 + - - +
84H LYS* 3.7 28.2 + - - +
85H GLN* 5.1 2.5 + - - +
53N GLN 2.8 22.1 + - - +
54N ALA* 3.8 7.6 - - - +
56N ALA* 1.3 71.3 - - - +
58N ILE* 1.3 56.7 + - - +
60N GLN* 3.4 15.6 + - - +
61N TYR* 3.0 27.7 + - - +
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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
----------------------------------------------------------
101G TYR* 3.6 29.4 - - + +
88H PHE* 6.5 0.4 - - + -
54N ALA* 3.2 20.7 + - + +
55N ILE* 3.1 11.6 + - + +
57N ASP* 1.3 72.7 - - - +
59N VAL* 1.3 61.3 + - - +
61N TYR* 3.1 8.3 + - + +
62N HIS* 2.8 47.9 + - + +
86N LEU* 3.7 28.5 - - + -
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Residues in contact with VAL 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N VAL* 4.0 8.7 - - + -
55N ILE 3.0 17.6 + - - +
56N ALA 3.7 6.5 - - - +
58N ILE* 1.3 70.6 - - - +
60N GLN* 1.3 62.2 + - - +
62N HIS* 3.1 2.2 + - - +
63N LEU* 2.8 47.0 + - + +
79N ALA 4.5 3.6 - - - +
82N VAL* 4.0 20.6 - - + -
83N PHE* 3.7 51.4 - - + +
86N LEU* 3.8 16.8 - - + -
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Residues in contact with GLN 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 TYR* 5.6 0.3 + - - -
2211 THR* 5.0 4.2 + - - -
2221 GLN* 6.2 2.2 - - - +
100G ARG* 3.9 28.8 + - - +
36N ARG* 4.0 31.7 + - - +
37N VAL* 3.9 28.3 - - + +
56N ALA 3.0 16.6 + - - +
57N ASP* 3.5 17.7 - - - +
59N VAL* 1.3 77.2 - - - +
61N TYR* 1.3 57.0 + - - +
63N LEU* 3.5 1.2 + - - +
64N GLU* 3.1 34.4 + - - +
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Residues in contact with TYR 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ALA* 5.0 2.6 + - - +
97G ALA* 3.4 44.6 - - + +
98G GLU* 3.6 17.2 + - + +
101G TYR* 3.7 30.3 - + + -
57N ASP 3.0 13.3 + - - +
58N ILE* 3.4 14.4 - - + +
59N VAL 3.1 0.2 - - - -
60N GLN* 1.3 74.5 - - - +
62N HIS* 1.3 91.2 + + - +
63N LEU 3.3 0.3 + - - -
64N GLU* 3.3 7.3 + - - +
65N LEU* 3.1 36.7 + - + +
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Residues in contact with HIS 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 3.9 29.3 - - + +
103F TYR* 4.2 12.5 + - + +
58N ILE* 2.8 40.2 + - + +
59N VAL 3.1 6.7 + - - +
61N TYR* 1.3 94.9 - + - +
63N LEU* 1.3 57.9 + - - +
65N LEU* 3.5 12.8 + - + +
66N TYR* 2.9 26.3 + - - +
82N VAL* 4.0 28.9 - - + -
86N LEU* 5.6 3.9 - - + +
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Residues in contact with LEU 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 5.5 0.9 - - + -
37N VAL* 3.8 30.1 - - + +
38N HIS* 4.4 6.5 - - + +
41N ILE* 4.3 12.3 - - + -
59N VAL* 2.8 33.9 + - + +
62N HIS* 1.3 72.1 - - - +
64N GLU* 1.3 59.7 + - - +
66N TYR* 3.5 7.0 - - + +
67N THR* 2.8 32.7 + - - -
74N PRO* 4.2 22.6 - - + +
78N THR* 4.5 5.4 - - + -
79N ALA* 3.8 36.6 - - + -
82N VAL* 4.2 18.2 - - + -
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Residues in contact with GLU 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G SER* 6.2 6.3 - - - -
72G ARG* 6.0 6.2 - - + +
96G ALA 4.3 1.6 - - - +
97G ALA* 3.9 17.2 - - + +
100G ARG* 3.5 37.6 + - - +
106G ASP* 4.7 6.9 - - - +
36N ARG* 5.8 1.6 + - - -
38N HIS* 5.2 2.9 + - - -
60N GLN* 3.1 23.8 + - - +
61N TYR* 3.6 7.6 - - - +
63N LEU* 1.3 73.5 - - - +
65N LEU* 1.3 65.0 + - - +
67N THR* 3.2 6.5 + - - +
68N SER* 3.1 28.2 + - - +
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Residues in contact with LEU 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 5.0 10.3 - - - +
93G LYS* 4.2 2.5 - - + +
94G ALA* 3.6 29.8 - - + +
97G ALA* 3.5 24.9 - - + +
61N TYR* 3.1 29.6 + - + +
62N HIS* 3.6 16.2 - - + +
64N GLU* 1.3 75.3 - - - +
66N TYR* 1.3 64.6 + - - +
67N THR 3.3 0.3 + - - -
68N SER* 3.3 8.8 - - - -
69N GLN* 3.3 45.6 + - - +
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Residues in contact with TYR 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 4.1 12.7 - + - -
103F TYR* 3.8 42.1 + + + -
105F THR* 4.4 12.6 - - - +
108F PRO* 5.1 5.7 - - - +
62N HIS 2.9 18.2 + - - +
63N LEU* 3.5 12.3 - - + +
64N GLU 3.3 0.2 - - - -
65N LEU* 1.3 77.0 - - - +
67N THR* 1.3 52.5 + - - +
69N GLN 3.3 0.3 + - - -
70N TYR* 2.7 70.1 + + + +
72N GLY 3.4 15.0 - - - -
73N THR 4.0 4.6 + - - -
74N PRO* 3.5 35.0 - - + +
75N SER 5.3 0.3 + - - -
78N THR* 4.0 12.2 + - + -
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Residues in contact with THR 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ARG* 4.6 16.6 - - - +
38N HIS* 3.0 30.6 - - + +
63N LEU 2.8 22.1 + - - -
64N GLU* 3.7 6.1 - - - -
65N LEU 3.2 0.2 - - - -
66N TYR* 1.3 73.5 - - - +
68N SER* 1.3 66.6 + - - +
69N GLN 3.2 0.9 + - - -
72N GLY* 3.0 31.3 + - - +
73N THR* 4.9 3.8 - - - +
74N PRO* 3.5 9.2 - - - +
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Residues in contact with SER 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G CYS* 3.9 10.7 - - - +
70G ILE 3.0 18.7 + - - -
71G SER* 4.5 4.6 - - - +
93G LYS* 3.0 49.5 + - - +
97G ALA* 5.8 0.7 - - - +
64N GLU* 3.1 15.7 + - - +
65N LEU* 3.3 14.1 - - - -
67N THR* 1.3 75.6 - - - +
69N GLN* 1.3 59.8 + - - -
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Residues in contact with GLN 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ASP* 5.5 1.4 - - - +
115F ARG* 5.2 1.7 + - - -
90G LEU* 3.6 32.6 - - + +
93G LYS* 4.0 19.6 + - + +
65N LEU* 3.3 45.7 + - - +
66N TYR 3.3 1.6 + - - -
67N THR 3.1 0.4 - - - -
68N SER* 1.3 81.3 - - - +
70N TYR* 1.3 107.7 + - + +
72N GLY 3.7 0.4 - - - -
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Residues in contact with TYR 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 3.7 19.3 - + + -
103F TYR* 4.5 8.3 - + - -
108F PRO* 5.5 6.9 - - + +
111F ALA* 3.5 39.0 - - + -
114F ASP* 6.4 1.1 - - + -
115F ARG* 3.0 29.9 + - - -
143F LYS* 5.9 0.9 + - - -
66N TYR* 2.7 61.3 + + + +
69N GLN* 1.3 116.0 + - + +
72N GLY* 1.3 62.7 + - - +
73N THR 4.1 0.9 + - - +
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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
----------------------------------------------------------
66N TYR* 3.4 7.1 - - - -
67N THR* 3.0 37.8 + - - -
69N GLN 3.7 0.6 - - - -
70N TYR* 1.3 81.5 - - - +
73N THR* 1.3 64.7 + - - -
74N PRO* 3.5 0.5 - - - +
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Residues in contact with THR 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LYS* 4.6 12.5 + - - -
38N HIS* 4.5 12.8 + - + +
66N TYR* 4.0 4.7 + - - -
67N THR* 4.7 4.8 - - - +
70N TYR 4.1 1.1 + - - +
72N GLY* 1.3 72.2 - - - -
74N PRO* 1.3 81.4 - - + +
75N SER 3.7 1.4 + - - -
105N ASP* 5.5 6.3 - - + +
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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