Contacts of the helix formed by residues 39 - 69 (chain C) in PDB entry 2VT4
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 GLN 39 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 1.3 65.9 + - - +
41C GLU* 4.3 16.0 - - + +
42C ALA* 3.0 35.3 + - + +
43C GLY 3.8 3.1 + - - -
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Residues in contact with TRP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN* 1.3 71.1 - - - +
41C GLU* 1.3 65.8 + - + +
42C ALA 3.3 0.3 + - - -
43C GLY* 3.6 2.1 + - - +
44C MET* 3.1 54.9 + - + +
102C VAL* 4.2 13.2 - - + -
103C VAL* 3.5 36.8 - - + -
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN* 3.1 15.5 - - + +
40C TRP* 1.3 90.6 - - + +
42C ALA* 1.3 56.6 + - - +
44C MET* 3.6 2.3 + - - +
45C SER* 2.8 39.5 + - - +
103C VAL* 3.8 24.5 - - + +
104C ARG* 5.2 12.9 + - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN* 3.0 30.0 + - + +
41C GLU* 1.3 79.0 - - - +
43C GLY* 1.3 63.3 + - - +
45C SER* 3.6 6.8 + - - -
46C LEU* 3.4 21.7 + - - +
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN 3.8 4.2 + - - -
40C TRP* 3.6 5.6 + - - -
41C GLU 3.5 0.2 - - - -
42C ALA* 1.3 76.6 - - - +
44C MET* 1.3 67.6 + - - +
46C LEU* 3.2 9.7 + - - +
47C LEU* 3.1 25.5 + - - +
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Residues in contact with MET 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 3.1 63.5 + - + +
41C GLU* 3.8 6.3 - - - +
42C ALA 3.3 0.4 - - - -
43C GLY* 1.3 75.5 - - - +
45C SER* 1.3 56.2 + - - +
46C LEU 3.0 4.5 - - - -
47C LEU* 3.5 5.8 + - - +
48C MET* 2.9 50.9 + - + +
102C VAL* 5.9 1.3 - - + -
103C VAL* 3.6 27.1 - - + +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 2.8 31.3 + - - +
42C ALA* 3.9 7.8 - - - -
44C MET* 1.3 76.2 - - - +
46C LEU* 1.3 59.5 + - - +
48C MET* 4.3 5.8 - - - -
49C ALA* 3.0 27.4 + - - +
103C VAL* 4.9 7.5 - - - +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA 3.4 13.1 + - - +
43C GLY* 3.2 13.9 + - - +
44C MET 3.0 0.6 - - - -
45C SER* 1.3 77.7 - - - +
47C LEU* 1.3 68.9 + - + +
48C MET 3.2 1.3 - - - -
49C ALA* 3.3 5.0 + - + +
50C LEU* 2.9 33.6 + - + +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY 3.1 13.3 + - - +
44C MET* 4.4 6.5 - - - +
46C LEU* 1.3 82.8 - - + +
48C MET* 1.3 69.5 + - + +
50C LEU* 3.0 23.7 + - + +
51C VAL* 3.0 30.5 + - + +
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Residues in contact with MET 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C MET* 2.9 51.7 + - + +
45C SER* 4.3 4.9 - - - -
47C LEU* 1.3 80.2 - - + +
49C ALA* 1.3 63.7 + - - +
51C VAL* 2.9 28.2 - - - +
52C VAL* 3.1 9.9 + - + +
95C VAL* 4.9 4.3 - - + -
99C ALA* 3.1 32.5 - - + +
102C VAL* 5.2 7.9 - - + -
103C VAL* 4.5 9.0 - - + -
330C TRP* 3.6 35.2 - - + -
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C SER 3.0 22.6 + - - +
46C LEU* 3.7 7.0 - - + +
48C MET* 1.3 78.8 - - - +
50C LEU* 1.3 60.3 + - - +
52C VAL* 3.7 9.3 + - - +
53C LEU* 3.3 19.9 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 2.9 20.5 + - + +
47C LEU* 3.2 27.6 - - + +
48C MET 3.0 0.4 - - - -
49C ALA* 1.3 76.2 - - - +
51C VAL* 1.3 68.0 + - + +
53C LEU* 3.1 19.6 + - + +
54C LEU* 3.0 28.9 + - + +
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.0 14.5 + - + +
48C MET* 2.9 27.6 - - - +
50C LEU* 1.3 73.9 - - + +
52C VAL* 1.3 80.0 - - - +
53C LEU 2.9 0.7 + - - -
54C LEU* 3.0 14.3 + - + +
55C ILE* 2.9 36.5 + - + +
95C VAL* 4.2 18.8 - - + -
330C TRP* 5.0 5.4 - - + -
337C ALA* 6.2 0.9 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET* 3.1 15.4 + - + +
49C ALA* 3.8 8.7 - - - +
51C VAL* 1.3 82.7 - - - +
53C LEU* 1.3 56.6 + - - +
55C ILE* 4.0 5.3 - - - +
56C VAL* 2.9 43.0 + - + +
91C GLY 3.4 23.6 - - - +
92C LEU* 5.7 1.3 - - + -
95C VAL* 3.6 26.7 - - + -
96C PRO* 4.2 13.0 - - + -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 3.3 12.1 + - - +
50C LEU* 3.1 23.5 + - + +
52C VAL* 1.3 78.8 - - - +
54C LEU* 1.3 62.1 + - + +
56C VAL* 4.8 2.7 - - + -
57C ALA* 2.8 47.2 + - + +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.0 19.0 + - + +
51C VAL* 3.0 15.8 + - + +
53C LEU* 1.3 77.3 - - + +
55C ILE* 1.3 64.6 + - - +
57C ALA* 5.0 1.3 - - - -
58C GLY* 2.8 25.8 + - - -
337C ALA* 4.1 21.3 - - + +
340C PRO* 5.5 0.3 - - - +
341C ILE* 5.1 19.1 - - + -
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Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 2.9 28.7 + - + +
52C VAL* 4.0 4.0 - - - +
54C LEU* 1.3 75.6 - - - +
56C VAL* 1.3 62.8 + - + +
59C ASN* 3.0 33.6 + - - +
87C ASP 3.3 26.9 - - - +
88C LEU* 4.4 0.4 - - - +
90C VAL* 4.8 0.2 - - + -
91C GLY* 3.5 22.4 - - - +
95C VAL* 4.4 16.8 - - + -
333C TYR 4.2 9.4 - - - +
334C ALA* 5.4 2.0 - - - -
336C SER* 3.8 24.5 - - - +
337C ALA* 3.4 28.2 - - + +
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 2.9 34.7 + - + +
53C LEU* 4.3 2.7 - - - +
55C ILE* 1.3 71.9 - - - +
57C ALA* 1.3 66.1 + - - +
60C VAL* 3.1 36.9 + - + +
88C LEU* 3.8 8.3 - - + +
91C GLY* 3.8 20.2 - - - +
92C LEU* 3.6 34.8 - - + -
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 2.8 35.1 + - + +
54C LEU* 4.0 1.8 - - - +
56C VAL* 1.3 74.3 - - - +
58C GLY* 1.3 62.1 + - - +
60C VAL* 3.3 4.8 + - - +
61C LEU* 3.0 30.6 + - + +
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU 2.8 19.8 + - - -
57C ALA* 1.3 74.9 - - - +
59C ASN* 1.3 55.4 + - - +
61C LEU* 3.3 11.4 - - - +
62C VAL* 3.2 29.8 + - - +
340C PRO* 3.2 26.7 - - - +
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Residues in contact with ASN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 3.0 26.6 + - - +
58C GLY* 1.3 74.6 - - - +
60C VAL* 1.3 64.6 + - - +
62C VAL* 3.7 7.1 + - - +
63C ILE* 3.3 29.8 + - - +
84C ALA* 3.5 28.6 - - + +
87C ASP* 3.5 21.4 - - + +
88C LEU* 3.9 13.9 - - + -
336C SER 2.9 28.3 + - - -
339C ASN* 4.8 2.3 - - - +
340C PRO* 3.8 18.1 - - - +
343C TYR* 6.0 0.2 - - - -
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.1 30.8 + - + +
57C ALA* 3.9 4.7 - - - +
59C ASN* 1.3 76.0 - - - +
61C LEU* 1.3 62.7 + - + +
63C ILE* 3.9 5.6 - - - +
64C ALA* 2.9 34.1 + - + +
88C LEU* 3.7 25.8 - - + -
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 3.0 19.4 + - - +
58C GLY* 3.3 11.4 - - - +
60C VAL* 1.3 77.9 - - + +
62C VAL* 1.3 60.2 + - + +
64C ALA* 3.8 4.6 - - + +
65C ALA* 2.8 32.7 + - + +
340C PRO* 6.3 1.1 - - + -
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY 3.2 15.1 + - - +
59C ASN* 3.8 9.6 - - - +
60C VAL 3.3 0.2 - - - -
61C LEU* 1.3 76.4 - - + +
63C ILE* 1.3 65.3 + - - +
64C ALA 3.1 0.9 + - - -
65C ALA* 3.1 5.3 + - - +
66C ILE* 3.1 42.0 + - + +
80C ILE* 4.1 17.7 - - + +
81C THR* 5.3 0.4 - - - -
84C ALA* 4.1 13.5 - - + -
340C PRO* 4.1 14.4 - - + -
343C TYR* 3.7 29.6 - - + -
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN 3.3 20.2 + - - +
60C VAL* 3.9 5.2 - - - +
62C VAL* 1.3 80.7 - - - +
64C ALA* 1.3 58.2 + - - +
66C ILE* 3.8 2.5 + - - +
67C GLY* 3.2 22.3 + - - -
81C THR* 3.8 27.0 + - + +
84C ALA* 3.7 23.3 - - + -
85C CYS* 4.0 22.9 - - - +
88C LEU* 4.2 20.4 - - + -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL* 2.9 23.3 + - + +
61C LEU* 3.9 6.1 - - + +
63C ILE* 1.3 78.9 - - + +
65C ALA* 1.3 60.0 + - - +
67C GLY* 3.2 2.5 + - - -
68C SER* 2.8 35.7 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 2.8 22.2 + - + +
62C VAL* 3.1 5.4 + - - +
64C ALA* 1.3 73.2 - - - +
66C ILE* 1.3 64.6 + - + +
68C SER* 3.1 14.6 + - - -
69C THR* 3.2 20.0 + - - -
72C LEU* 3.8 18.9 - - + +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.1 32.2 + - + +
63C ILE 4.2 2.9 - - - +
65C ALA* 1.3 76.1 - - + +
67C GLY* 1.3 59.3 + - - +
69C THR 2.9 21.0 - - - +
72C LEU* 4.2 25.6 - - + +
73C GLN* 3.4 26.5 - - + +
77C ASN* 3.5 43.3 - - + +
78C LEU* 5.5 4.0 - - + -
80C ILE* 4.2 8.3 - - + -
81C THR* 3.6 18.8 - - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE 3.2 17.0 + - - -
64C ALA* 3.2 4.5 + - - -
66C ILE* 1.3 79.1 - - - +
68C SER* 1.3 61.4 + - - +
69C THR 5.0 0.3 - - - -
70C GLN* 6.0 0.2 - - - +
73C GLN* 4.4 13.4 + - - -
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 2.8 23.9 + - - +
65C ALA* 3.1 8.3 + - - -
67C GLY* 1.3 79.6 - - - +
69C THR* 1.3 68.7 + - - +
70C GLN* 3.6 8.0 + - - +
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA 3.2 8.9 + - - -
66C ILE 2.9 24.0 - - - +
67C GLY 5.0 0.2 - - - -
68C SER* 1.3 77.8 - - - +
70C GLN* 1.3 58.8 + - - +
71C ARG* 3.3 34.3 - - + +
72C LEU* 3.6 22.3 + - + +
73C GLN* 3.3 9.2 + - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il