Contacts of the helix formed by residues 38 - 62 (chain B) in PDB entry 4BPU
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.3 0.4 - - - -
37B ILE* 1.3 78.1 - - - +
39B LEU* 1.3 53.1 + - - +
40B ILE* 3.6 9.0 + - - +
41B GLU* 3.2 28.7 + - - +
42B PHE* 2.7 33.9 + - - +
92C ASN* 5.6 2.5 - - - -
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Residues in contact with LEU 39 (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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13B LEU* 3.9 25.9 - - + +
38B SER* 1.3 72.0 - - - +
40B ILE* 1.3 62.7 + - + +
42B PHE* 3.3 19.3 - - + +
43B GLU* 3.0 44.3 + - - +
245B ARG* 4.2 23.6 - - + +
57C TYR* 3.7 27.8 - - + +
91C HIS* 3.6 26.2 - - + +
92C ASN* 5.1 3.5 + - - +
96C LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.2 7.8 + - - +
39B LEU* 1.3 76.0 - - + +
41B GLU* 1.3 62.0 + - - +
43B GLU* 3.3 15.1 - - + +
44B ASN* 2.9 47.0 + - - +
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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
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36B ASN 4.9 0.5 - - - +
37B ILE* 3.7 23.0 - - + +
38B SER* 3.2 20.2 + - - +
40B ILE* 1.3 78.8 - - - +
42B PHE* 1.3 55.2 + - - +
44B ASN* 3.7 5.8 - - + +
45B LEU* 2.7 53.3 + - + +
97B ARG* 2.5 39.6 + - - -
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.0 2.2 - - + -
13B LEU* 3.3 24.0 - - + -
37B ILE* 3.7 10.4 - - + +
38B SER 2.7 18.5 + - - +
39B LEU* 3.3 19.3 - - + +
41B GLU* 1.3 77.2 - - - +
43B GLU* 1.3 71.0 + - + +
45B LEU* 3.6 2.7 - - - +
46B ALA* 3.0 23.9 + - - +
105B ILE* 3.4 51.4 - - + +
108B LEU* 4.9 0.2 - - + -
245B ARG 4.4 9.6 - - - -
246B LEU* 3.6 26.7 - - + -
249B LEU* 5.1 4.3 - - + -
96C LEU* 3.3 39.3 - - + -
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Residues in contact with GLU 43 (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 LEU* 3.0 36.8 + - - +
40B ILE* 3.3 16.5 - - + +
42B PHE* 1.3 85.0 - - + +
44B ASN* 1.3 66.6 + - - +
46B ALA* 3.3 5.3 + - - +
47B ILE* 2.9 45.4 + - + +
245B ARG 5.1 2.7 - - - +
248B PRO* 4.5 25.2 - - + +
249B LEU* 5.5 5.8 - - + +
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Residues in contact with ASN 44 (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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40B ILE* 2.9 33.6 + - - +
41B GLU* 3.7 6.7 - - + +
43B GLU* 1.3 83.4 - - - +
45B LEU* 1.3 57.5 + - - +
47B ILE* 3.4 12.0 + - - +
48B ASP* 2.9 40.8 + - - +
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Residues in contact with LEU 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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37B ILE* 5.0 2.7 - - + -
41B GLU* 2.7 40.4 + - + +
42B PHE 3.6 4.3 - - - +
44B ASN* 1.3 69.8 - - - +
46B ALA* 1.3 66.6 + - - +
48B ASP* 3.3 5.2 + - - +
49B ARG* 2.9 23.7 + - - +
83B PHE* 4.6 2.2 - - + -
97B ARG* 5.4 0.4 - - - +
98B ARG* 3.5 55.6 - - + +
101B ILE* 3.6 41.3 - - + -
102B SER* 3.8 17.8 - - - +
105B ILE* 4.4 5.4 - - + -
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Residues in contact with ALA 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 PHE* 3.0 17.2 + - + +
43B GLU* 3.7 6.3 - - - +
45B LEU* 1.3 77.3 - - - +
47B ILE* 1.3 58.2 + - - +
49B ARG* 3.1 2.2 + - - -
50B VAL* 2.9 34.9 + - - +
102B SER* 5.2 1.1 - - - -
105B ILE* 3.7 25.7 - - + +
106B LEU* 3.7 11.5 - - + +
249B LEU* 3.5 26.2 - - + -
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Residues in contact with ILE 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 GLU* 2.9 33.6 + - + +
44B ASN* 3.7 13.0 - - - +
46B ALA* 1.3 75.1 - - - +
48B ASP* 1.3 66.8 + - - +
50B VAL* 3.3 9.0 + - - +
51B LYS* 2.9 40.1 + - + +
248B PRO* 5.2 9.4 - - + +
249B LEU* 5.0 10.1 - - + -
252B HIS* 3.9 37.5 - - + +
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Residues in contact with ASP 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 ASN* 2.9 30.7 + - - +
45B LEU* 3.4 6.0 - - - +
46B ALA 3.2 0.2 - - - -
47B ILE* 1.3 79.8 - - - +
49B ARG* 1.3 58.8 + - - +
51B LYS* 3.1 13.9 + - - +
52B LEU* 2.9 24.4 + - - +
81B LEU* 4.0 19.1 - - + +
82B LYS* 4.0 15.4 + - - -
83B PHE* 4.0 16.6 - - + -
98B ARG* 3.7 25.9 + - - +
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Residues in contact with ARG 49 (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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29B TYR* 3.8 10.9 + - - -
45B LEU 2.9 9.2 + - - +
46B ALA 3.9 0.7 - - - +
48B ASP* 1.3 73.8 - - - +
50B VAL* 1.3 62.1 + - - +
52B LEU* 3.1 15.6 + - + +
53B LEU* 2.8 33.9 + - + +
83B PHE* 3.9 11.7 - - + -
99B ASP* 2.9 39.6 + - - +
102B SER* 2.6 62.7 + - - -
103B HIS* 3.6 6.8 - - - +
106B LEU* 3.6 20.0 - - + -
124B GLU* 2.4 36.4 + - - -
127B LEU* 3.6 14.3 - - - +
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Residues in contact with VAL 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 ALA 2.9 18.7 + - - +
47B ILE* 3.5 10.1 - - + +
49B ARG* 1.3 75.3 - - - +
51B LYS* 1.3 64.6 + - + +
53B LEU* 3.4 3.9 + - - +
54B LYS* 2.9 36.9 + - + +
106B LEU* 3.6 26.7 - - + -
110B TYR* 3.9 21.5 - - + +
119B TRP* 5.1 0.2 - - - -
249B LEU* 4.0 14.1 - - + -
252B HIS* 3.2 31.2 - - + +
253B LEU* 4.6 2.7 - - + -
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Residues in contact with LYS 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 ILE* 2.9 29.4 + - + +
48B ASP* 3.1 13.7 + - - +
50B VAL* 1.3 78.1 - - + +
52B LEU* 1.3 51.5 + - - +
54B LYS* 3.2 9.2 + - + +
55B SER* 2.8 40.6 + - - +
81B LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 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 ASP 2.9 11.2 + - - +
49B ARG* 3.3 24.2 - - + +
51B LYS* 1.3 75.4 - - - +
53B LEU* 1.3 62.7 + - + +
55B SER* 2.9 7.2 + - - -
56B VAL* 2.8 42.5 + - + +
74B LEU* 4.6 6.3 - - + -
77B GLU* 5.1 3.4 - - + -
78B LEU* 4.0 30.1 - - + +
81B LEU* 3.4 24.3 - - + +
83B PHE* 3.6 25.4 - - + -
99B ASP* 4.9 0.4 - - - +
127B LEU* 3.9 24.7 - - + -
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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
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49B ARG* 2.8 27.8 + - + +
50B VAL* 3.9 3.4 - - - +
52B LEU* 1.3 84.0 - - + +
54B LYS* 1.3 59.1 + - - +
56B VAL* 3.1 6.6 + - + +
57B GLU* 2.8 23.7 + - - +
106B LEU* 3.8 13.2 - - + -
110B TYR* 5.2 0.2 - - + -
119B TRP* 3.8 23.1 - - + -
120B PHE* 3.7 24.5 - - + +
123B GLN* 3.3 33.2 - - + +
124B GLU* 3.2 34.5 - - - +
127B LEU* 4.6 5.8 - - + -
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Residues in contact with LYS 54 (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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50B VAL* 2.9 27.3 + - + +
51B LYS* 3.6 7.2 - - + +
53B LEU* 1.3 76.0 - - - +
55B SER* 1.3 51.5 + - - +
57B GLU* 3.2 14.8 + - - +
58B ASN* 2.7 41.5 + - - +
110B TYR* 5.2 0.4 - - - -
119B TRP* 4.1 17.5 - - + -
252B HIS* 3.0 14.6 + - - +
253B LEU* 2.8 41.1 + - - -
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Residues in contact with SER 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 LYS* 2.8 18.3 + - - +
52B LEU* 3.2 10.1 - - - -
54B LYS* 1.3 73.4 - - - +
56B VAL* 1.3 58.9 + - - +
57B GLU 3.0 1.3 - - - -
58B ASN* 2.8 31.8 + - - +
59B LEU* 2.8 25.1 + - - +
74B LEU* 5.9 0.7 - - - -
77B GLU* 3.5 38.7 + - - +
81B LEU* 4.7 0.5 - - - +
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Residues in contact with VAL 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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52B LEU* 2.8 31.8 + - + +
53B LEU* 3.1 11.9 + - + +
55B SER* 1.3 75.2 - - - +
57B GLU* 1.3 61.8 + - - +
59B LEU* 3.5 8.5 + - + +
60B GLY* 3.2 17.8 + - - -
70B TYR* 5.0 8.2 + - - +
74B LEU* 4.0 26.7 - - + +
123B GLN* 3.9 25.5 - - + +
126B ASP* 4.0 20.5 - - + +
127B LEU* 4.5 17.5 - - + +
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Residues in contact with GLU 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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53B LEU 2.8 12.9 + - - +
54B LYS* 3.3 16.5 - - - +
55B SER 3.0 0.2 - - - -
56B VAL* 1.3 76.9 - - - +
58B ASN* 1.3 65.6 + - - +
60B GLY* 3.2 10.8 + - - +
61B VAL* 3.6 19.4 + - + +
119B TRP* 3.1 36.3 + - + -
122B GLN* 5.9 0.9 - - - +
123B GLN* 3.7 19.5 + - - +
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Residues in contact with ASN 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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54B LYS* 2.7 27.0 + - - +
55B SER* 2.8 21.5 + - - +
57B GLU* 1.3 75.7 - - - +
59B LEU* 1.3 62.2 + - + +
60B GLY 3.2 0.2 - - - -
61B VAL* 3.5 5.3 + - - +
62B SER* 3.2 32.0 + - - +
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Residues in contact with LEU 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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55B SER* 2.8 21.6 + - - +
56B VAL* 3.9 6.1 - - + +
57B GLU 3.3 0.2 - - - -
58B ASN* 1.3 81.2 - - + +
60B GLY* 1.3 59.4 + - - +
61B VAL 3.4 0.4 - - - -
62B SER* 4.1 6.1 - - - -
63B TYR* 3.4 52.0 + - + +
70B TYR* 3.9 27.9 - - + +
73B LYS* 4.1 11.2 - - + -
74B LEU* 3.5 53.8 - - + +
77B GLU* 5.6 1.6 - - + -
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Residues in contact with GLY 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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56B VAL 3.2 9.7 + - - -
57B GLU* 3.2 7.9 + - - -
58B ASN 3.2 1.2 - - - -
59B LEU* 1.3 79.5 - - - +
61B VAL* 1.3 62.1 + - - +
63B TYR 4.0 8.1 - - - +
70B TYR* 5.3 3.8 - - - -
126B ASP* 6.1 1.3 - - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.7 17.7 - - + +
58B ASN* 3.5 6.1 + - - +
60B GLY* 1.3 80.7 - - - +
62B SER* 1.3 66.2 + - - +
63B TYR 4.7 0.4 - - - +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.2 17.4 + - - +
59B LEU* 4.5 3.6 - - - -
61B VAL* 1.3 82.2 - - - +
63B TYR* 1.3 89.0 + - - +
64B VAL* 5.4 0.7 - - - +
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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
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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