Contacts of the helix formed by residues 48 - 71 (chain b) in PDB entry 5GJQ
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 THR 48 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47b GLY* 1.3 68.9 - - - -
49b ALA* 1.3 67.4 + - - +
50b ALA 4.3 1.3 - - - +
51b ASP* 3.0 36.3 + - - +
52b THR* 3.0 21.4 + - - +
95b GLY* 2.6 23.5 + - - -
99c ARG* 5.0 3.3 + - - +
125c ASP* 5.8 2.0 - - - +
127c ILE* 4.2 16.6 - - + -
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Residues in contact with ALA 49 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b GLY 3.1 9.1 + - - +
48b THR* 1.3 72.5 - - - +
50b ALA* 1.3 63.7 + - - +
52b THR* 2.6 23.9 + - - -
53b ASP* 2.9 14.9 + - - +
125c ASP* 4.7 4.8 + - - +
129c CYS* 3.7 25.8 - - + -
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Residues in contact with ALA 50 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48b THR* 3.3 1.6 - - - +
49b ALA* 1.3 78.7 - - - +
51b ASP* 1.3 58.5 + - - +
53b ASP* 3.3 4.3 + - - +
54b MET* 2.9 35.3 + - - +
96c TYR* 4.5 3.6 - - + -
125c ASP* 4.4 3.0 + - - +
127c ILE* 3.7 33.9 - - + +
128c GLY 4.0 5.2 - - - +
129c CYS* 3.6 35.0 - - + +
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Residues in contact with ASP 51 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48b THR* 3.0 23.6 + - - +
50b ALA* 1.3 74.5 - - - +
52b THR* 1.3 56.7 + - - +
54b MET* 4.1 0.7 - - - +
55b THR* 2.4 39.2 + - - -
94b ILE* 3.6 18.3 - - + -
95b GLY 3.0 26.5 + - - +
96b ALA* 4.5 1.3 - - - -
96c TYR* 2.9 29.3 + - - -
99c ARG* 3.0 32.7 + - - -
127c ILE* 3.9 3.6 - - - +
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Residues in contact with THR 52 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35b HIS* 4.7 6.9 + - - -
45b GLY* 4.5 9.7 - - - -
46b ALA 3.1 31.8 - - - +
48b THR 3.0 9.2 + - - +
49b ALA* 2.6 25.8 + - - -
51b ASP* 1.3 73.6 - - - +
53b ASP* 1.3 67.0 + - - +
55b THR* 4.0 4.4 - - - -
56b THR* 3.0 29.2 + - - +
96b ALA* 3.7 18.2 - - + -
97b ALA 3.9 2.0 - - - +
98b LEU* 4.1 16.4 - - + +
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Residues in contact with ASP 53 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32b SER 5.3 0.5 - - - +
35b HIS* 3.0 27.6 + - - -
49b ALA* 2.9 15.5 + - - +
50b ALA* 3.6 7.2 - - - +
52b THR* 1.3 84.1 + - - +
54b MET* 1.3 60.7 + - - +
56b THR* 3.4 4.3 - - - +
57b GLN* 2.9 47.4 + - - +
129c CYS* 3.8 10.6 - - - -
130c PRO* 3.8 28.2 - - + +
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Residues in contact with MET 54 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU 5.6 2.9 - - - +
50b ALA* 2.9 24.4 + - - +
51b ASP 4.1 1.3 - - - +
53b ASP* 1.3 72.9 - - - +
55b THR* 1.3 67.3 + - - +
57b GLN* 3.4 29.8 + - - +
58b LEU* 2.9 24.6 + - - +
86b MET* 5.5 0.9 - - - -
92c ALA* 4.7 6.3 - - + +
93c ASN* 4.6 22.0 - - - +
96c TYR* 3.8 56.5 - - + +
128c GLY 4.7 13.2 - - - +
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Residues in contact with THR 55 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51b ASP 2.4 27.0 + - - -
52b THR* 4.0 4.9 - - - -
54b MET* 1.3 78.9 - - - +
56b THR* 1.3 64.6 + - - +
58b LEU* 3.2 2.4 + - - +
59b ILE* 3.1 26.5 + - - +
83b LEU* 3.5 26.5 - - + -
86b MET* 3.9 31.4 - - + +
87b LEU* 4.6 6.5 - - + -
94b ILE* 3.8 17.3 - - - +
96b ALA* 4.0 12.5 - - + +
98b LEU* 4.6 2.5 - - + -
96c TYR* 5.4 0.5 + - - -
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Residues in contact with THR 56 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35b HIS* 3.6 35.7 - - + +
36b PHE 4.8 2.0 - - - +
37b ILE* 3.1 26.7 - - + +
43b CYS* 3.8 18.4 - - - +
52b THR 3.0 16.6 + - - +
53b ASP* 3.4 11.2 - - - +
55b THR* 1.3 79.6 - - - +
57b GLN* 1.3 64.4 + - + +
59b ILE* 4.5 3.4 - - - -
60b SER* 3.0 28.1 + - - -
83b LEU* 5.2 2.1 - - - +
98b LEU* 5.1 6.0 - - - +
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Residues in contact with GLN 57 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TYR* 6.0 1.9 - - - -
98C LEU* 4.0 20.2 - - + +
101C GLN* 3.4 45.1 + - - +
53b ASP* 2.9 32.6 + - - +
54b MET* 3.7 31.8 - - - +
56b THR* 1.3 79.2 - - + +
58b LEU* 1.3 67.2 + - - +
60b SER* 3.2 7.5 + - - -
61b SER* 2.9 23.0 + - - -
130c PRO* 5.8 5.1 - - - +
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Residues in contact with LEU 58 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 4.0 27.9 - - + +
54b MET 2.9 14.2 + - - +
55b THR* 3.2 8.9 + - - +
57b GLN* 1.3 77.0 - - - +
59b ILE* 1.3 66.4 + - + +
61b SER* 3.2 4.4 + - - -
62b ASN* 2.9 44.9 + - - +
86b MET* 3.8 36.6 - - + -
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Residues in contact with ILE 59 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37b ILE* 4.0 23.8 - - + -
55b THR* 3.1 17.4 + - + +
56b THR* 3.9 5.2 - - - +
58b LEU* 1.3 90.6 - - + +
60b SER* 1.3 68.0 + - - +
62b ASN* 3.3 4.9 + - - +
63b LEU* 3.0 26.2 + - + +
79b ALA* 4.3 20.2 - - + -
82b MET* 3.4 35.3 - - + +
83b LEU* 3.4 34.8 - - + +
86b MET* 4.7 2.0 - - - -
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Residues in contact with SER 60 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LYS* 6.0 0.3 + - - -
97C TYR* 5.5 8.7 - - - -
36b PHE* 3.8 24.0 + - - -
37b ILE* 2.8 33.6 + - - +
56b THR 3.0 19.7 + - - -
57b GLN* 3.2 6.7 + - - -
59b ILE* 1.3 78.2 - - - +
61b SER* 1.3 56.4 + - - +
63b LEU* 3.4 2.3 + - - +
64b GLU* 2.9 29.9 + - - +
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Residues in contact with SER 61 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLN* 2.8 47.1 + - - +
97C TYR* 5.5 9.0 - - - -
98C LEU* 3.9 25.2 - - - +
57b GLN 2.9 13.2 + - - -
58b LEU* 3.4 8.9 - - - +
59b ILE 3.2 0.2 - - - -
60b SER* 1.3 76.5 - - - +
62b ASN* 1.3 68.8 + - - +
64b GLU* 3.0 2.0 + - - -
65b LEU* 3.0 15.9 + - - +
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Residues in contact with ASN 62 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 5.5 1.8 + - - +
58b LEU* 2.9 45.0 + - - +
59b ILE* 4.1 5.4 - - - +
61b SER* 1.3 79.1 + - - +
63b LEU* 1.3 56.9 + - - +
65b LEU* 3.4 10.3 + - - +
66b HIS* 2.9 27.9 + - - +
82b MET* 4.0 25.9 - - + +
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Residues in contact with LEU 63 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37b ILE* 3.5 32.3 - - + +
38b SER* 4.3 4.9 - - - -
41b ILE* 4.1 14.4 - - + -
59b ILE 3.0 16.5 + - - +
60b SER* 3.7 4.5 - - - +
62b ASN* 1.3 74.9 - - - +
64b GLU* 1.3 61.1 + - - +
66b HIS* 3.6 8.5 - - + +
67b SER* 2.8 31.4 + - - +
74b PRO* 3.9 23.5 - - + +
78b THR* 3.8 30.3 - - + -
79b ALA* 3.9 19.1 - - + -
82b MET* 4.1 10.5 - - + -
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Residues in contact with GLU 64 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE 4.2 0.2 - - - +
68C THR* 3.9 19.1 - - - +
69C LYS* 3.7 34.0 + - + -
90C ARG 5.2 0.3 - - - +
94C GLN* 2.6 50.2 + - - +
97C TYR* 4.9 4.2 - - - -
37b ILE 5.5 0.4 + - - -
60b SER* 2.9 14.8 + - - +
61b SER 3.0 1.1 + - - +
63b LEU* 1.3 71.2 - - - +
65b LEU* 1.3 67.3 + - - +
67b SER* 3.1 8.5 + - - +
68b LEU* 3.0 45.4 + - + +
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Residues in contact with LEU 65 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 4.5 16.6 - - + +
90C ARG* 3.5 32.6 - - + +
91C LYS* 4.4 29.4 - - + +
94C GLN* 3.6 26.0 - - + -
61b SER 3.0 11.2 + - - +
62b ASN* 3.5 14.8 - - - +
64b GLU* 1.3 77.9 - - - +
66b HIS* 1.3 58.9 + - - +
68b LEU* 3.3 10.8 + - + +
69b SER* 3.0 30.6 + - - -
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Residues in contact with HIS 66 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.7 33.5 - + - -
105B TYR* 3.4 54.0 + + + -
113B MET* 5.2 5.8 - - + -
62b ASN 2.9 17.8 + - - +
63b LEU* 3.6 14.1 - - + +
64b GLU 3.2 0.2 - - - -
65b LEU* 1.3 79.0 - - - +
67b SER* 1.3 57.0 + - - +
69b SER* 3.3 6.6 + - - -
70b THR* 2.8 43.5 + - + +
74b PRO* 6.3 2.0 - - + -
78b THR* 4.8 8.3 - - + -
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Residues in contact with SER 67 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39b PRO* 6.2 0.2 - - - +
63b LEU 2.8 17.1 + - - -
64b GLU* 3.1 13.7 + - - +
66b HIS* 1.3 71.1 - - - +
68b LEU* 1.3 63.9 + - - +
70b THR* 3.3 8.5 + - - -
71b GLY* 2.7 33.6 + - - -
72b ARG 3.4 17.9 + - - +
74b PRO* 3.7 22.2 - - - +
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Residues in contact with LEU 68 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 5.1 0.9 - - - +
66C PRO* 4.1 23.3 - - + +
67C ILE 3.1 26.5 - - - +
68C THR* 4.7 8.7 - - - +
90C ARG* 3.5 50.9 + - + +
64b GLU* 3.0 33.1 + - + +
65b LEU* 3.3 8.7 - - + +
67b SER* 1.3 84.7 + - - +
69b SER* 1.3 61.4 + - - +
71b GLY* 3.8 6.5 + - - -
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Residues in contact with SER 69 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 4.9 1.9 - - - +
113B MET* 2.7 40.0 - - - +
116B LYS* 4.8 15.5 + - - +
90C ARG* 4.3 12.1 - - - +
65b LEU* 3.0 17.2 + - - -
66b HIS* 3.6 9.8 + - - -
68b LEU* 1.3 78.9 - - - +
70b THR* 1.3 61.3 + - - +
71b GLY 3.6 0.2 + - - -
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Residues in contact with THR 70 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 4.8 6.1 - - + -
110B PRO* 5.7 1.6 - - + -
112B ASP* 4.5 5.0 - - - +
113B MET* 3.8 32.8 - - + -
147B GLN* 5.8 0.2 + - - -
66b HIS* 2.8 39.8 + - + +
67b SER* 3.3 10.4 + - - -
69b SER* 1.3 76.7 - - - +
71b GLY* 1.3 62.1 + - - +
72b ARG* 3.1 42.7 + - - +
73b LEU 5.5 0.9 + - - -
74b PRO* 6.0 0.5 - - - +
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Residues in contact with GLY 71 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67b SER 2.7 19.0 + - - -
68b LEU 3.8 5.8 + - - -
69b SER 3.3 3.0 - - - -
70b THR* 1.3 72.7 - - - +
72b ARG* 1.3 58.6 + - - +
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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
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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) + - + + + + + -
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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