Contacts of the helix formed by residues 29 - 56 (chain B) in PDB entry 5VBL
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 ALA 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY* 1.3 72.1 - - - -
30B LEU* 1.4 62.4 + - - +
32B PRO* 3.6 5.5 - - - +
33B ALA* 3.3 25.3 + - - +
90B TYR* 3.9 22.4 - - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY* 3.4 3.2 - - - -
29B ALA* 1.4 74.2 - - - +
31B ILE* 1.4 66.0 + - + +
33B ALA* 3.4 6.3 + - - +
34B ILE* 3.2 46.5 + - + +
293B TYR* 4.0 30.1 - - + +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.8 20.0 - - - -
28B GLY 4.6 1.7 + - - +
30B LEU* 1.4 75.6 - - + +
32B PRO* 1.4 68.0 - - + +
34B ILE* 3.2 10.5 + - + +
35B TYR* 3.1 55.4 + - + +
89B THR* 4.1 17.0 - - + -
292B PRO* 3.8 37.0 - - + +
293B TYR* 3.8 35.4 - - + -
296B CYS* 4.3 9.2 - - + -
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Residues in contact with PRO 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY 3.4 22.9 - - - +
29B ALA 3.6 7.6 - - - +
31B ILE* 1.4 92.7 - - + +
33B ALA* 1.4 59.5 + - - +
35B TYR* 3.5 5.2 + - + +
36B MET* 3.3 27.7 + - - +
86B ALA* 3.5 35.2 - - + +
89B THR* 4.3 7.9 - - + -
90B TYR* 3.9 28.0 - - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 3.3 19.4 + - - +
30B LEU* 3.6 5.4 - - - +
31B ILE 3.3 0.8 - - - -
32B PRO* 1.4 75.2 - - - +
34B ILE* 1.4 65.4 + - + +
36B MET* 3.4 9.0 + - - +
37B LEU* 3.2 30.2 + - + +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.2 43.0 + - + +
31B ILE* 3.2 5.3 + - + +
33B ALA* 1.4 74.2 - - + +
35B TYR* 1.4 53.9 + - + +
37B LEU* 3.0 13.3 + - + +
38B VAL* 2.8 41.2 + - + +
296B CYS* 3.7 31.0 - - - -
300B VAL* 3.8 22.9 - - + -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 4.3 13.5 - - + -
31B ILE* 3.1 36.1 + - + +
32B PRO 3.6 8.5 - - - +
34B ILE* 1.4 78.6 - - + +
36B MET* 1.3 56.4 + - - +
38B VAL* 3.7 6.5 + - + +
39B PHE* 3.2 25.6 + - - +
82B LEU* 3.7 30.5 - - + +
85B TRP* 4.3 3.1 - - + -
86B ALA* 3.8 31.2 - - + -
89B THR* 3.8 14.6 - - + -
292B PRO 4.2 0.2 + - - -
295B THR* 3.5 19.9 + - - -
296B CYS* 3.7 27.8 - - + -
299B TYR* 3.6 35.1 - + + -
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Residues in contact with MET 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO 3.3 15.8 + - - +
33B ALA* 3.7 10.1 - - - +
34B ILE 3.2 0.4 - - - -
35B TYR* 1.3 73.6 - - - +
37B LEU* 1.4 59.6 + - - +
39B PHE* 3.3 18.1 + - + +
40B LEU* 3.0 27.8 + - - +
83B PRO* 3.7 41.5 - - + +
86B ALA* 4.2 7.9 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.2 21.2 + - + +
34B ILE* 3.0 14.0 + - + +
36B MET* 1.4 73.2 - - - +
38B VAL* 1.4 59.9 + - + +
40B LEU* 3.4 11.3 + - + +
41B LEU* 2.9 61.5 + - + +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 2.8 28.7 + - + +
35B TYR* 4.0 8.7 - - + +
36B MET 3.4 0.2 - - - -
37B LEU* 1.4 69.4 - - + +
39B PHE* 1.4 54.6 + - - +
41B LEU* 6.2 0.2 - - + -
42B GLY* 2.8 30.8 + - - -
79B VAL* 3.6 6.2 - - + +
82B LEU* 3.8 16.6 - - + -
299B TYR 3.4 24.9 - - - +
300B VAL* 3.8 31.6 - - + +
303B CYS* 3.7 30.8 - - + +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR 3.2 15.2 + - - +
36B MET* 3.4 21.3 - - + +
37B LEU 3.3 0.2 - - - -
38B VAL* 1.4 75.7 - - - +
40B LEU* 1.3 61.8 + - + +
43B THR* 2.7 58.6 + - + -
79B VAL* 3.2 36.9 - - - +
80B VAL* 4.0 17.0 - - + -
82B LEU* 4.4 1.1 - - + +
83B PRO* 3.7 29.8 - - + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B MET 3.0 16.2 + - - +
37B LEU* 3.4 12.1 + - + +
39B PHE* 1.3 86.4 - - + +
41B LEU* 1.3 70.5 + - + +
43B THR* 3.3 12.4 + - - +
44B THR* 2.8 28.6 + - + +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 2.9 43.9 + - + +
40B LEU* 1.3 86.0 - - + +
42B GLY* 1.3 58.3 + - - +
44B THR* 3.9 4.4 + - - +
45B GLY* 3.0 27.1 + - - -
303B CYS* 4.0 26.4 - - + +
306B PRO* 5.2 0.5 - - - +
307B PHE* 3.7 36.0 - - + -
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Residues in contact with GLY 42 (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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38B VAL 2.8 20.7 + - - -
39B PHE 3.9 0.2 - - - -
41B LEU* 1.3 76.5 - - - +
43B THR* 1.4 58.7 + - - +
46B ASN* 3.1 39.9 + - - +
76B LEU* 3.9 2.9 - - - +
79B VAL* 3.7 16.3 - - - +
303B CYS* 3.7 11.6 - - - +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 2.7 48.3 + - + +
40B LEU* 3.3 10.9 + - - +
42B GLY* 1.4 73.9 - - - +
44B THR* 1.3 64.4 + - - +
47B GLY* 3.2 24.4 + - - -
76B LEU* 3.4 17.2 - - + +
79B VAL* 3.6 13.9 - - + +
80B VAL* 4.2 13.9 - - + -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 2.8 27.2 + - + +
41B LEU* 3.9 5.4 + - - +
43B THR* 1.3 78.0 + - - +
45B GLY* 1.3 60.6 + - - +
47B GLY* 4.0 0.6 - - - -
48B LEU* 3.1 30.1 + - - +
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Residues in contact with GLY 45 (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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41B LEU 3.0 22.5 + - - -
44B THR* 1.3 75.0 + - - +
46B ASN* 1.4 59.4 + - - +
48B LEU* 3.2 22.1 + - - +
49B VAL* 3.2 16.5 + - - +
306B PRO* 3.5 21.0 - - - +
307B PHE* 6.6 0.2 - - - -
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Residues in contact with ASN 46 (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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42B GLY* 3.1 30.7 + - - +
45B GLY* 1.4 71.5 - - - +
47B GLY* 1.3 58.8 + - - +
49B VAL* 3.3 10.0 + - - +
50B LEU* 3.0 32.9 + - - +
72B ALA* 3.6 32.0 - - - +
75B ASP* 3.5 26.3 - - - +
76B LEU* 4.2 8.7 - - + -
302B SER 3.0 26.2 + - - +
305B ASN* 5.2 2.3 + - - +
306B PRO* 4.0 14.3 - - - +
309B TYR* 6.1 0.5 - - - -
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Residues in contact with GLY 47 (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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43B THR 3.2 21.0 + - - -
44B THR* 4.0 1.3 - - - -
45B GLY 3.2 0.2 - - - -
46B ASN* 1.3 75.7 - - - +
48B LEU* 1.4 57.2 + - - +
50B LEU* 3.7 8.9 + - - +
51B TRP* 3.1 28.1 + - - +
76B LEU* 4.1 7.7 - - - +
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Residues in contact with LEU 48 (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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44B THR 3.1 18.7 + - - +
45B GLY* 3.2 9.1 + - - +
47B GLY* 1.4 74.4 - - - +
49B VAL* 1.4 61.5 + - - +
51B TRP* 3.5 14.6 - - + +
52B THR* 3.3 30.4 + - + +
306B PRO* 6.5 0.4 - - + -
316B PHE* 4.0 10.0 - - + -
320B CYS* 3.8 29.2 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.2 15.4 + - - +
46B ASN* 3.3 11.8 + - - +
48B LEU* 1.4 76.4 - - - +
50B LEU* 1.4 61.2 + - - +
52B THR* 2.7 21.3 + - - -
53B VAL* 3.2 15.7 + - + +
68B ILE* 3.9 28.9 - - + +
69B ALA* 5.4 0.4 - - - +
72B ALA* 3.9 16.6 - - + -
306B PRO* 4.0 20.6 - - + -
309B TYR* 4.1 16.2 - - + -
316B PHE* 3.7 20.2 - - + -
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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
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46B ASN 3.0 20.2 + - - +
47B GLY* 3.9 7.4 - - - +
48B LEU 3.5 0.2 - - - -
49B VAL* 1.4 73.6 - - - +
51B TRP* 1.3 62.7 + - - +
53B VAL* 4.8 3.1 - - - +
54B PHE* 3.3 57.1 + - + +
69B ALA* 3.5 23.6 - - - +
72B ALA* 3.8 14.4 - - + -
73B VAL* 3.7 22.0 - - + -
76B LEU* 4.1 25.4 - - + -
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Residues in contact with TRP 51 (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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47B GLY 3.1 18.9 + - - +
48B LEU* 3.5 18.2 - - + +
49B VAL 3.2 0.2 - - - -
50B LEU* 1.3 77.1 - - - +
52B THR* 1.4 63.3 + - + +
54B PHE* 4.2 1.0 - - - +
55B ARG* 2.9 52.5 + - + +
319B ALA 5.9 0.9 - - - -
323B MET* 3.5 52.0 - - + +
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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
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48B LEU* 3.3 14.5 + - + +
49B VAL 2.7 20.8 + - - -
51B TRP* 1.4 83.9 - - + +
53B VAL* 1.3 63.5 + - - +
55B ARG* 3.4 20.5 - - - +
56B SER* 3.7 12.3 + - - -
315B ARG* 5.7 1.6 + - - -
316B PHE* 3.6 18.0 - - + -
319B ALA* 3.8 31.9 - - + +
320B CYS* 3.8 25.4 - - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.2 19.5 + - + +
50B LEU 4.5 2.7 - - - +
52B THR* 1.3 80.0 + - - +
54B PHE* 1.3 62.7 + - + +
56B SER* 3.0 26.0 + - - +
61B ARG* 3.5 16.4 + - - +
65B ASP* 3.8 44.0 - - + +
68B ILE* 4.5 21.3 - - + -
69B ALA* 4.1 16.8 - - + -
315B ARG* 6.2 2.0 - - - +
316B PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.3 50.3 + - + +
51B TRP* 4.2 1.3 - - - +
53B VAL* 1.3 81.0 - - + +
55B ARG* 1.4 63.1 + - - +
56B SER 3.4 0.4 + - - -
57B SER* 4.2 6.1 + - - -
61B ARG* 3.5 30.6 + - - +
69B ALA* 4.3 13.5 - - + -
73B VAL* 5.9 1.1 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 2.9 34.4 + - + +
52B THR* 3.4 16.8 - - - +
54B PHE* 1.4 76.3 - - - +
56B SER* 1.3 66.9 + - - +
57B SER* 3.3 8.7 + - - -
319B ALA* 4.3 18.5 + - - +
322B SER* 3.7 29.9 + - - -
323B MET* 3.5 38.2 - - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR 3.8 13.5 - - - -
53B VAL* 3.0 17.2 + - - +
54B PHE 3.4 0.6 - - - -
55B ARG* 1.3 82.4 - - - +
57B SER* 1.3 59.0 + - - +
60B LYS* 3.9 10.4 - - - +
61B ARG* 3.2 16.8 + - - +
315B ARG* 3.2 29.9 + - - -
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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