Contacts of the helix formed by residues 38 - 63 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE* 1.3 76.8 - - - +
39D LEU* 1.3 59.3 + - - +
40D ILE* 3.6 8.4 + - - +
41D GLU* 3.2 26.1 + - - +
42D PHE* 2.8 28.3 + - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.8 19.7 - - + +
91A HIS* 3.8 27.1 - - + -
92A ASN* 5.9 0.6 + - - +
96A LEU* 6.5 0.4 - - + -
38D SER* 1.3 74.1 - - - +
40D ILE* 1.3 60.9 + - + +
42D PHE* 3.3 19.1 - - + +
43D GLU* 2.9 45.0 + - + +
245D ARG* 3.8 51.1 - - + +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D SER* 3.2 8.2 - - - +
39D LEU* 1.3 76.8 - - + +
41D GLU* 1.3 60.4 + - - +
43D GLU* 3.3 15.4 - - - +
44D ASN* 2.9 47.6 + - - +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN 4.6 1.0 - - - +
37D ILE* 3.3 32.7 - - + +
38D SER* 3.2 19.0 + - - +
40D ILE* 1.3 77.0 - - - +
42D PHE* 1.3 57.5 + - - +
44D ASN* 3.7 4.8 - - + +
45D LEU* 2.8 53.1 + - + +
97D ARG* 2.5 40.4 + - - -
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 6.3 3.1 - - + -
37D ILE* 3.8 18.7 - - + +
38D SER 2.8 18.4 + - - +
39D LEU* 3.3 23.3 - - + +
41D GLU* 1.3 77.1 - - - +
43D GLU* 1.3 69.5 + - + +
45D LEU* 3.6 2.1 - - - +
46D ALA* 3.0 25.4 + - + +
105D ILE* 3.4 48.7 - - + +
108D LEU* 4.5 9.0 - - + -
245D ARG 4.8 5.8 - - - -
246D LEU* 3.5 33.2 - - + -
249D LEU* 3.8 15.7 - - + -
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 2.9 37.7 + - + +
40D ILE* 3.3 23.3 - - - +
42D PHE* 1.3 84.1 - - + +
44D ASN* 1.3 63.2 + - - +
46D ALA* 3.3 5.0 + - - +
47D ILE* 2.9 45.2 + - + +
245D ARG 5.5 1.6 - - - +
248D PRO* 5.7 8.7 - - + +
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE* 2.9 34.3 + - - +
41D GLU* 3.7 5.6 - - - +
43D GLU* 1.3 83.5 - - - +
45D LEU* 1.3 58.3 + - - +
47D ILE* 3.4 11.4 + - - +
48D ASP* 2.9 41.3 + - - +
98D ARG* 6.1 1.1 - - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 5.4 0.9 - - + -
41D GLU* 2.8 43.4 + - + +
42D PHE 3.6 3.8 - - - +
44D ASN* 1.3 70.3 - - - +
46D ALA* 1.3 66.4 + - - +
48D ASP* 3.3 3.8 + - - +
49D ARG* 3.0 24.3 + - - +
83D PHE* 4.6 0.9 - - + -
98D ARG* 3.5 64.6 - - + +
101D ILE* 3.6 38.4 - - + -
102D SER* 3.8 13.1 - - - -
105D ILE* 4.3 6.3 - - + -
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.0 17.3 + - + +
43D GLU* 3.7 7.4 - - - +
45D LEU* 1.3 77.1 - - - +
47D ILE* 1.3 63.2 + - + +
49D ARG* 3.2 2.0 + - - -
50D VAL* 2.9 30.3 + - + +
102D SER 5.2 0.9 - - - -
105D ILE* 3.7 24.6 - - + +
106D LEU* 3.7 18.8 - - + +
249D LEU* 4.1 13.5 - - + -
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLU* 2.9 33.4 + - + +
44D ASN* 3.7 12.3 - - - +
46D ALA* 1.3 75.4 - - + +
48D ASP* 1.3 67.0 + - - +
50D VAL* 3.3 8.7 + - - +
51D LYS* 3.0 39.3 + - + +
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASN* 2.9 27.6 + - - +
45D LEU 3.6 6.1 - - - +
47D ILE* 1.3 80.1 - - - +
49D ARG* 1.3 62.9 + - - +
51D LYS* 3.1 14.7 + - - +
52D LEU 3.0 17.3 + - - -
81D LEU* 3.7 26.8 - - + +
82D LYS* 4.4 10.8 + - - -
83D PHE* 4.1 8.5 - - + -
98D ARG* 3.4 35.2 + - - +
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.0 26.7 + - - -
45D LEU 3.0 16.8 + - - +
46D ALA 3.9 0.9 - - - +
48D ASP* 1.3 76.9 - - - +
50D VAL* 1.3 57.2 + - - +
52D LEU* 3.1 6.8 + - + +
53D LEU* 2.9 34.6 + - + +
83D PHE* 3.9 16.3 - - + -
99D ASP* 2.8 29.3 + - - +
102D SER* 2.7 54.6 + - - +
103D HIS* 3.6 7.7 - - - +
106D LEU* 3.8 19.5 - - + -
124D GLU* 2.5 34.5 + - - -
127D LEU* 3.9 13.7 - - - +
131D ARG* 4.6 1.0 - - - +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 2.9 23.4 + - + +
47D ILE* 3.5 7.9 - - - +
49D ARG* 1.3 76.7 - - - +
51D LYS* 1.3 65.2 + - + +
53D LEU* 3.3 3.7 + - - +
54D LYS* 3.0 44.0 + - + +
106D LEU* 3.6 27.1 - - + -
110D TYR* 4.1 21.5 - - + +
119D TRP* 5.0 0.2 - - - -
249D LEU* 5.6 2.9 - - + -
252D HIS 5.4 8.7 - - - +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.0 31.0 + - + +
48D ASP* 3.3 14.5 + - - +
50D VAL* 1.3 76.6 - - + +
52D LEU* 1.3 66.4 + - - +
54D LYS* 3.2 5.4 + - - +
55D SER* 2.9 27.7 + - - +
81D LEU* 3.8 26.5 - - + +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ASP 3.0 8.7 + - - +
49D ARG* 3.1 19.0 + - + +
51D LYS* 1.3 76.8 - - - +
53D LEU* 1.3 64.5 + - + +
55D SER* 2.9 9.9 + - - -
56D VAL* 2.8 42.5 + - + +
74D LEU* 4.6 4.7 - - + -
77D GLU* 4.9 1.3 - - + -
78D LEU* 3.6 45.3 - - + +
81D LEU* 3.5 22.5 - - + +
83D PHE* 3.6 20.4 - - + -
127D LEU* 4.1 18.4 - - + -
131D ARG* 4.5 3.1 - - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 2.9 31.8 + - + +
50D VAL* 3.9 2.9 - - - +
52D LEU* 1.3 79.4 - - + +
54D LYS* 1.3 57.9 + - - +
56D VAL* 3.1 6.6 + - + -
57D GLU 2.9 23.6 + - - -
106D LEU* 3.7 13.5 - - + -
110D TYR* 5.2 0.2 - - + -
119D TRP* 3.7 23.3 - - + -
120D PHE* 3.5 25.6 - - + -
123D GLN* 3.2 31.5 - - + +
124D GLU* 3.5 31.9 - - - +
127D LEU* 4.5 10.8 - - + -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 3.0 34.5 + - + +
51D LYS* 3.8 6.3 - - - +
53D LEU* 1.3 76.9 - - - +
55D SER* 1.3 57.2 + - - +
57D GLU* 3.3 8.3 + - - +
58D ASN* 2.9 36.8 + - - +
110D TYR* 5.0 4.0 - - - -
119D TRP* 3.9 26.5 - - + -
252D HIS 5.7 3.0 + - - -
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Residues in contact with SER 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 2.9 17.8 + - - +
52D LEU* 3.2 9.9 - - - -
54D LYS* 1.3 73.9 - - - +
56D VAL* 1.3 66.2 + - - +
58D ASN* 2.9 13.4 + - - +
59D LEU* 2.9 33.7 + - - +
74D LEU* 5.6 0.7 - - - -
77D GLU* 3.2 40.5 + - - +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 2.8 29.9 + - + +
53D LEU* 3.1 11.6 + - + +
55D SER* 1.3 75.7 - - - +
57D GLU* 1.3 62.3 + - - +
59D LEU* 3.6 4.0 + - - +
60D GLY* 3.3 17.7 + - - -
70D TYR* 4.2 9.7 + - - +
74D LEU* 3.7 26.5 - - + -
123D GLN* 3.8 17.2 - - + +
126D ASP* 3.5 35.2 - - + +
127D LEU* 4.2 17.9 - - + +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU 2.9 11.3 + - - +
54D LYS* 3.5 12.2 - - - +
55D SER 3.1 0.2 - - - -
56D VAL* 1.3 79.0 - - - +
58D ASN* 1.3 63.8 + - - +
60D GLY* 3.3 9.5 + - - -
61D VAL* 3.5 21.8 + - + +
119D TRP* 3.0 37.4 + - - -
122D GLN* 5.4 3.7 + - - +
123D GLN* 3.3 23.0 + - + +
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Residues in contact with ASN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LYS* 2.9 24.9 + - - +
55D SER* 2.9 12.8 + - - +
57D GLU* 1.3 80.9 - - - +
59D LEU* 1.3 61.6 + - + +
60D GLY 3.1 0.2 - - - -
61D VAL* 3.3 7.3 + - - +
62D SER* 2.9 33.0 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D SER* 2.9 22.1 + - - +
56D VAL* 4.2 3.1 - - - +
58D ASN* 1.3 79.9 - - + +
60D GLY* 1.3 57.6 + - - +
61D VAL 3.3 0.2 - - - -
62D SER* 3.9 9.6 - - - +
63D TYR* 3.2 32.8 + - + +
70D TYR* 3.1 33.7 - - + +
73D LYS* 4.0 19.1 - - + +
74D LEU* 3.5 53.6 - - + +
77D GLU* 5.4 2.5 - - + +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL 3.3 12.1 + - - -
57D GLU* 3.3 4.9 + - - -
58D ASN 3.1 1.4 - - - -
59D LEU* 1.3 78.2 - - - +
61D VAL* 1.3 61.8 + - - +
63D TYR 3.3 13.0 - - - +
64D VAL* 5.3 0.6 - - - -
65D LYS* 5.1 11.6 + - - -
70D TYR* 4.4 7.4 - - - -
126D ASP* 5.1 2.9 - - - -
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.5 21.5 - - + +
58D ASN* 3.3 7.0 + - - +
60D GLY* 1.3 79.6 - - - +
62D SER* 1.3 66.6 + - - +
63D TYR 4.2 0.7 - - - +
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Residues in contact with SER 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ASN* 2.9 20.9 + - - +
59D LEU* 4.4 7.6 - - - +
61D VAL* 1.3 81.9 - - - +
63D TYR* 1.3 82.2 + - - +
64D VAL* 5.5 0.5 - - - +
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.2 24.3 + - + +
60D GLY 3.3 21.1 - - - +
61D VAL 4.2 1.0 - - - +
62D SER* 1.3 96.3 - - - +
64D VAL* 1.3 76.9 + - - +
67D THR* 4.3 7.6 - - + +
69D GLN* 3.6 43.3 + - + +
70D TYR* 3.5 32.1 - + + -
73D LYS* 4.1 23.2 - - + +
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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) + - + + + + + -
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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