Contacts of the helix formed by residues 39 - 69 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 1.3 55.8 + - - +
41B GLU* 2.7 14.5 - - + +
42B ALA* 2.7 43.1 + - + +
43B GLY 4.0 1.4 + - - -
108D LEU 3.5 21.7 + - - -
109D TRP* 3.4 22.1 - - - +
110D GLY* 4.1 12.2 - - - +
113D LEU* 5.9 0.2 - - - +
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Residues in contact with TRP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 1.3 75.0 - - - +
41B GLU* 1.3 64.0 + - + +
42B ALA 3.1 0.8 + - - -
43B GLY* 3.6 3.0 + - - +
44B MET* 3.1 55.3 + - + +
102B VAL* 4.2 13.2 - - + -
103B VAL* 3.5 36.8 - - + -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 2.7 10.1 - - + +
40B TRP* 1.3 90.1 - - + +
42B ALA* 1.3 56.5 + - - +
44B MET* 3.6 2.3 + - - +
45B SER* 2.8 39.7 + - - +
103B VAL* 3.8 24.1 - - + +
104B ARG* 5.2 4.7 - - - -
110D GLY* 3.6 9.3 - - - -
111D SER* 3.1 40.4 + - - -
112D PHE* 4.5 3.1 + - - +
196D PRO* 3.5 26.1 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 2.7 36.3 + - + +
41B GLU* 1.3 72.2 - - - +
43B GLY* 1.3 61.9 + - - +
45B SER* 3.6 7.2 + - - -
46B LEU* 3.4 21.7 + - - +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN 4.0 2.4 + - - -
40B TRP* 3.6 6.2 + - - +
41B GLU 3.5 0.2 - - - -
42B ALA* 1.3 75.9 - - - +
44B MET* 1.3 67.2 + - - +
46B LEU* 3.2 10.5 + - - +
47B LEU* 3.1 25.1 + - - +
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 3.1 62.6 + - + +
41B GLU* 3.8 5.8 - - - +
42B ALA 3.3 0.4 - - - -
43B GLY* 1.3 75.3 - - - +
45B SER* 1.3 56.6 + - - +
46B LEU 3.0 4.0 - - - -
47B LEU* 3.5 6.0 + - - +
48B MET* 2.9 50.6 + - + +
102B VAL* 5.9 1.3 - - + -
103B VAL* 3.6 27.6 - - + +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 2.8 31.8 + - - +
42B ALA* 3.9 7.6 - - - -
44B MET* 1.3 75.5 - - - +
46B LEU* 1.3 59.1 + - - +
48B MET* 4.3 6.5 - - - -
49B ALA* 3.0 27.4 + - - +
103B VAL* 4.9 7.1 - - - +
196D PRO* 5.7 2.6 - - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 3.4 12.7 + - - +
43B GLY* 3.2 13.4 + - - +
44B MET 3.0 1.0 - - - -
45B SER* 1.3 78.4 - - - +
47B LEU* 1.3 72.8 + - + +
48B MET 3.2 1.1 - - - -
49B ALA* 3.3 5.1 + - + +
50B LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 3.1 13.5 + - - +
44B MET* 4.3 6.5 - - - +
46B LEU* 1.3 83.2 - - + +
48B MET* 1.3 69.0 + - + +
50B LEU* 3.0 24.2 + - + +
51B VAL* 3.0 30.0 + - + +
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B MET* 2.9 51.7 + - + +
45B SER* 4.3 5.4 - - - -
47B LEU* 1.3 79.5 - - + +
49B ALA* 1.3 64.0 + - - +
51B VAL* 3.0 27.6 - - - +
52B VAL* 3.1 10.1 + - + +
95B VAL* 4.9 4.0 - - + -
99B ALA* 3.1 32.8 - - + +
102B VAL* 5.2 7.4 - - + -
103B VAL* 4.5 9.0 - - + -
330B TRP* 3.7 34.8 - - + -
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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
----------------------------------------------------------
45B SER 3.0 22.0 + - - +
46B LEU* 3.7 6.7 - - + +
48B MET* 1.3 78.3 - - - +
50B LEU* 1.3 61.1 + - - +
52B VAL* 3.8 10.0 + - - +
53B LEU* 3.3 19.6 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.0 20.7 + - + +
47B LEU* 3.2 28.7 - - + +
48B MET 3.0 0.4 - - - -
49B ALA* 1.3 76.7 - - - +
51B VAL* 1.3 67.6 + - + +
53B LEU* 3.1 19.4 + - + +
54B LEU* 3.0 28.7 + - + +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.0 15.0 + - + +
48B MET* 3.0 26.7 - - - +
50B LEU* 1.3 75.5 - - + +
52B VAL* 1.3 78.5 - - - +
53B LEU 3.0 0.9 + - - -
54B LEU* 3.0 15.3 + - + +
55B ILE* 2.9 36.1 + - + +
95B VAL* 4.2 19.1 - - + -
330B TRP* 5.0 5.4 - - + -
337B ALA* 6.2 0.9 - - + -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 3.1 16.2 + - + +
49B ALA* 3.8 9.0 - - - +
51B VAL* 1.3 82.3 - - - +
53B LEU* 1.3 56.6 + - - +
55B ILE* 4.1 5.6 - - - +
56B VAL* 2.9 42.6 + - + +
91B GLY 3.4 24.2 - - - +
92B LEU* 5.7 1.1 - - + -
95B VAL* 3.6 26.5 - - + -
96B PRO* 4.2 12.8 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.3 12.1 + - - +
50B LEU* 3.1 23.3 + - + +
52B VAL* 1.3 77.9 - - - +
54B LEU* 1.3 62.5 + - + +
56B VAL* 4.8 2.5 - - + -
57B ALA* 2.8 48.5 + - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.0 18.6 + - + +
51B VAL* 3.0 16.3 + - + +
53B LEU* 1.3 76.3 - - + +
55B ILE* 1.3 64.5 + - - +
57B ALA* 5.0 1.3 - - - -
58B GLY* 2.8 25.6 + - - -
337B ALA* 4.1 21.5 - - + +
340B PRO* 5.5 0.3 - - - +
341B ILE* 5.1 19.3 - - + -
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 2.9 28.1 + - + +
52B VAL* 4.1 3.4 - - - +
54B LEU* 1.3 75.8 - - - +
56B VAL* 1.3 64.3 + - + +
59B ASN* 3.0 33.4 + - - +
87B ASP 3.3 26.5 - - - +
88B LEU* 4.4 0.4 - - - +
90B VAL* 4.8 0.2 - - + -
91B GLY* 3.5 23.3 - - - +
95B VAL* 4.4 16.6 - - + -
333B TYR 4.2 9.6 - - - +
334B ALA* 5.4 2.0 - - - -
336B SER* 3.8 23.8 - - - +
337B ALA* 3.4 28.2 - - + +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 2.9 34.4 + - + +
53B LEU* 4.3 2.7 - - - +
55B ILE* 1.3 71.2 - - - +
57B ALA* 1.3 65.3 + - - +
60B VAL* 3.1 36.6 + - + +
88B LEU* 3.8 9.3 - - + +
91B GLY* 3.8 20.4 - - - +
92B LEU* 3.6 34.5 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 2.8 35.3 + - + +
54B LEU* 4.1 1.8 - - - +
56B VAL* 1.3 74.1 - - - +
58B GLY* 1.3 62.0 + - - +
60B VAL* 3.3 5.1 + - - +
61B LEU* 3.0 30.6 + - + +
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU 2.8 19.8 + - - -
57B ALA* 1.3 74.5 - - - +
59B ASN* 1.3 56.0 + - - +
61B LEU* 3.3 11.2 - - - +
62B VAL* 3.2 29.6 + - - +
340B PRO* 3.2 26.7 - - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.0 26.7 + - - +
58B GLY* 1.3 74.6 - - - +
60B VAL* 1.3 65.0 + - - +
62B VAL* 3.7 6.9 + - - +
63B ILE* 3.3 29.7 + - - +
84B ALA* 3.5 23.3 - - + +
87B ASP* 3.5 26.2 - - + +
88B LEU* 3.9 13.7 - - + -
336B SER 2.9 28.1 + - - -
339B ASN* 4.8 2.3 - - - +
340B PRO* 3.8 18.5 - - - +
343B TYR* 6.0 0.2 - - - -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.1 30.4 + - + +
57B ALA* 3.9 4.7 - - - +
59B ASN* 1.3 75.3 - - - +
61B LEU* 1.3 62.3 + - + +
63B ILE* 3.9 5.9 - - - +
64B ALA* 2.9 34.0 + - + +
88B LEU* 3.7 26.0 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 3.0 19.2 + - - +
58B GLY* 3.3 11.0 - - - +
60B VAL* 1.3 78.3 - - + +
62B VAL* 1.3 60.0 + - - +
64B ALA* 3.8 4.2 - - + +
65B ALA* 2.8 32.3 + - - +
340B PRO* 6.3 1.1 - - + -
353B PHE* 3.7 32.1 - - + +
356B LEU* 4.3 26.1 - - + +
357B LEU* 4.1 35.4 - - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 3.2 15.8 + - - +
59B ASN* 3.8 10.1 - - - +
60B VAL 3.3 0.2 - - - -
61B LEU* 1.3 75.5 - - - +
63B ILE* 1.3 65.4 + - - +
64B ALA 3.1 0.3 + - - -
65B ALA* 3.1 6.2 + - - +
66B ILE* 3.1 42.5 + - + +
80B ILE* 4.1 17.7 - - + +
81B THR* 5.3 0.4 - - - -
84B ALA* 4.1 13.9 - - + -
340B PRO* 4.1 14.1 - - + -
343B TYR* 3.7 29.2 - - + -
349B PHE* 5.6 4.0 - - + -
353B PHE* 4.5 9.9 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN 3.3 19.7 + - - +
60B VAL* 3.9 5.4 - - - +
62B VAL* 1.3 80.0 - - - +
64B ALA* 1.3 58.2 + - + +
66B ILE* 3.8 2.1 + - - +
67B GLY* 3.2 22.7 + - - -
81B THR* 3.8 27.0 + - + +
84B ALA* 3.7 22.4 - - + -
85B CYS* 3.9 23.3 - - - +
88B LEU* 4.2 20.6 - - + -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 2.9 23.1 + - + +
61B LEU* 3.9 4.9 - - + +
63B ILE* 1.3 78.3 - - + +
65B ALA* 1.3 59.4 + - - +
67B GLY* 3.2 2.5 + - - -
68B SER* 2.8 34.5 + - - +
356B LEU* 4.5 16.4 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU 2.8 22.3 + - - +
62B VAL* 3.7 4.9 - - - +
64B ALA* 1.3 72.2 - - - +
66B ILE* 1.3 63.2 + - - +
68B SER* 3.1 12.4 + - - -
69B THR* 3.2 19.6 + - - -
72B LEU* 3.8 19.1 - - + +
349B PHE* 4.9 6.3 - - + -
352B ALA* 4.1 17.9 - - + +
353B PHE* 5.0 5.2 - - + -
356B LEU* 4.1 14.9 - - + +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.1 32.0 + - + +
63B ILE 4.2 2.9 - - - +
65B ALA* 1.3 76.5 - - - +
67B GLY* 1.3 59.1 + - - +
69B THR 2.9 20.6 - - - +
72B LEU* 4.1 17.7 - - + +
73B GLN* 3.4 25.9 - - + +
77B ASN* 3.5 39.7 - - + +
78B LEU* 5.5 4.0 - - + -
80B ILE* 4.2 8.3 - - + -
81B THR* 3.6 18.2 - - - +
349B PHE* 4.2 18.4 - - + -
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 3.2 17.2 + - - -
64B ALA* 3.2 4.7 + - - -
66B ILE* 1.3 78.7 - - - +
68B SER* 1.3 61.6 + - - +
69B THR 5.0 0.3 - - - -
70B GLN* 6.0 0.2 - - - +
73B GLN* 4.4 13.2 + - - -
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 2.8 23.2 + - - +
65B ALA* 3.1 7.8 + - - -
67B GLY* 1.3 79.4 - - - +
69B THR* 1.3 67.6 + - - +
70B GLN* 3.6 8.1 + - - +
356B LEU* 4.0 17.1 - - - +
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 3.2 8.9 + - - -
66B ILE 2.9 20.8 - - - +
67B GLY 5.0 0.2 - - - -
68B SER* 1.3 76.4 - - - +
70B GLN* 1.3 58.8 + - - +
71B ARG* 3.3 34.3 - - + +
72B LEU* 3.6 22.7 + - + +
73B GLN* 3.3 8.9 + - - -
352B ALA* 4.6 8.5 - - - +
355B ARG* 5.1 13.9 + - - +
----------------------------------------------------------
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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