Contacts of the helix formed by residues 32 - 58 (chain z) in PDB entry 4IL6
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 ASP 32 (chain z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42y ARG* 5.8 4.0 - - - +
31z GLN* 1.3 83.3 - - + +
33z TRP* 1.3 61.7 + - - +
34z ASP* 3.4 3.4 - - - +
35z ARG* 3.4 28.0 + - - +
36z SER* 2.9 28.3 + - - +
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Residues in contact with TRP 33 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135c ARG* 3.9 25.9 - - - +
521c LMG 3.3 38.8 + - + -
26z ALA 3.9 17.3 - - - -
27z TYR* 3.6 40.6 - + - -
29z SER* 4.7 5.6 - - - +
30z PRO 4.0 14.4 - - - +
31z GLN 3.3 1.4 - - - -
32z ASP* 1.3 75.5 - - - +
34z ASP* 1.3 67.4 + - - +
35z ARG 3.4 0.2 - - - -
36z SER* 4.1 4.9 - - - -
37z LYS* 2.8 65.0 + - + +
40z ILE* 4.0 14.4 - - + -
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Residues in contact with ASP 34 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32z ASP* 3.4 1.3 - - - -
33z TRP* 1.3 90.6 + - - +
35z ARG* 1.3 61.6 + - - +
37z LYS* 3.6 7.1 + - - +
38z GLN* 3.5 18.9 + - - +
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Residues in contact with ARG 35 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32z ASP* 3.4 27.5 + - - +
34z ASP* 1.3 77.9 - - - +
36z SER* 1.3 63.3 + - - +
38z GLN* 2.8 35.9 + - - +
39z LEU* 3.2 56.7 + - - +
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Residues in contact with SER 36 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42y ARG* 5.3 5.7 + - - -
26z ALA* 3.9 27.3 - - - +
29z SER* 6.0 0.9 - - - -
32z ASP* 2.9 26.3 + - - +
33z TRP* 3.3 11.6 + - - -
34z ASP 3.3 0.4 - - - -
35z ARG* 1.3 76.5 - - - +
37z LYS* 1.3 59.7 + - - +
39z LEU* 3.1 10.6 + - - +
40z ILE* 2.9 36.0 + - - +
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Residues in contact with LYS 37 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521c LMG 3.4 61.8 + - + -
33z TRP* 2.8 53.7 + - + +
34z ASP* 3.9 6.5 - - - +
35z ARG 3.5 0.2 - - - -
36z SER* 1.3 71.1 - - - +
38z GLN* 1.3 59.0 + - - +
40z ILE* 3.4 5.6 + - - +
41z PHE* 3.0 46.4 + - + -
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Residues in contact with GLN 38 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34z ASP 3.5 11.0 + - - +
35z ARG* 2.8 38.0 + - - +
36z SER 3.3 0.6 - - - -
37z LYS* 1.3 78.2 - - - +
39z LEU* 1.3 57.9 + - - +
41z PHE* 3.4 8.4 + - + +
42z LEU* 2.9 41.4 + - + +
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Residues in contact with LEU 39 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19z MET* 5.1 1.4 - - - +
35z ARG* 3.2 50.2 + - - +
36z SER* 3.1 12.4 + - - +
38z GLN* 1.3 76.7 - - - +
40z ILE* 1.3 55.7 + - + +
42z LEU* 3.8 12.4 - - + +
43z GLY* 2.7 33.4 + - - -
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Residues in contact with ILE 40 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127c PHE* 3.7 31.2 - - + -
521c LMG 3.9 13.0 - - + -
19z MET* 4.0 7.2 - - - +
22z GLY 5.8 0.7 - - - -
23z VAL* 4.2 20.6 - - + +
26z ALA* 3.8 26.7 - - + -
27z TYR* 4.0 24.9 - - + +
33z TRP* 4.0 10.8 - - + -
36z SER 2.9 21.0 + - - +
37z LYS* 3.7 5.8 - - - +
39z LEU* 1.3 72.2 - - + +
41z PHE* 1.3 56.2 + - - +
43z GLY 3.4 0.2 + - - -
44z SER* 2.7 39.0 + - - +
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Residues in contact with PHE 41 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521c LMG 3.2 75.4 - - + -
37z LYS* 3.0 37.8 + - + +
38z GLN* 3.5 12.1 - - + +
40z ILE* 1.3 77.4 - - - +
42z LEU* 1.3 57.2 + - - +
44z SER* 3.7 5.4 - - - -
45z GLY* 3.1 24.4 + - - -
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Residues in contact with LEU 42 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38z GLN* 2.9 30.0 + - + +
39z LEU* 3.8 13.9 - - + +
41z PHE* 1.3 72.7 - - - +
43z GLY* 1.3 61.1 + - - +
45z GLY* 3.3 2.2 + - - -
46z LEU* 3.0 41.4 + - + +
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Residues in contact with GLY 43 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15z LEU* 3.8 15.7 - - - +
19z MET* 3.8 19.5 - - - +
39z LEU 2.7 21.7 + - - -
40z ILE 3.8 0.9 - - - -
42z LEU* 1.3 74.7 - - - +
44z SER* 1.3 55.8 + - - +
46z LEU* 3.5 3.7 + - - +
47z TRP* 2.9 30.3 + - - +
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Residues in contact with SER 44 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127c PHE* 3.7 18.5 - - - -
521c LMG 4.0 34.7 - - - +
19z MET* 3.4 17.0 - - - +
40z ILE* 2.7 27.8 + - - +
41z PHE 3.7 5.2 - - - -
43z GLY* 1.3 72.5 - - - +
45z GLY* 1.3 58.3 + - - +
47z TRP* 3.5 3.1 + - - +
48z ILE* 3.1 36.3 + - - +
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Residues in contact with GLY 45 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41z PHE 3.1 13.9 + - - -
42z LEU* 3.8 3.4 - - - -
43z GLY 3.3 0.2 - - - -
44z SER* 1.3 74.9 - - - +
46z LEU* 1.3 58.6 + - - +
48z ILE* 3.4 9.1 + - - +
49z ALA* 3.0 28.7 + - - +
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Residues in contact with LEU 46 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15z LEU* 3.9 25.1 - - + -
42z LEU* 3.0 26.7 + - + +
43z GLY* 3.9 4.7 - - - +
45z GLY* 1.3 72.5 - - - +
47z TRP* 1.3 61.3 + - - +
49z ALA* 3.3 10.7 + - + +
50z LEU* 2.8 45.6 + - + +
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Residues in contact with TRP 47 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120c ILE* 3.6 23.3 - - + -
123c ALA* 3.6 29.6 - - + -
124c VAL* 4.8 1.8 - - + -
521c LMG 3.5 64.6 - - + +
101k BCR 4.3 14.3 - - + +
12z LEU* 3.7 21.7 - - + +
15z LEU* 3.6 18.3 - - + +
16z SER* 2.8 31.4 + - - -
19z MET* 5.4 0.7 - - + -
43z GLY 2.9 18.6 + - - +
44z SER* 3.7 7.0 - - - +
45z GLY 3.3 0.2 - - - -
46z LEU* 1.3 74.0 - - - +
48z ILE* 1.3 72.5 + - + +
50z LEU* 3.2 2.1 + - - -
51z VAL* 3.1 43.7 + - + +
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Residues in contact with ILE 48 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521c LMG 3.8 72.9 - - + +
44z SER 3.1 21.1 + - - +
45z GLY* 3.7 7.2 - - - +
47z TRP* 1.3 87.3 - - + +
49z ALA* 1.3 61.9 + - - +
51z VAL* 3.5 4.1 + - - +
52z LEU* 3.3 34.9 + - + +
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Residues in contact with ALA 49 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45z GLY 3.0 15.0 + - - +
46z LEU* 3.4 17.0 - - + +
47z TRP 3.1 0.2 - - - -
48z ILE* 1.3 77.8 - - - +
50z LEU* 1.3 57.8 + - + +
52z LEU* 3.2 12.0 + - - +
53z VAL* 2.9 35.8 + - + +
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Residues in contact with LEU 50 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8z ALA* 3.5 31.4 - - + +
11z ALA* 3.9 15.7 - - + +
12z LEU* 3.8 28.3 - - + +
15z LEU* 3.8 24.5 - - + -
46z LEU* 2.8 38.9 + - + +
47z TRP 3.2 4.2 + - - +
49z ALA* 1.3 71.2 - - + +
51z VAL* 1.3 56.3 + - - +
53z VAL* 3.6 8.9 - - + +
54z VAL* 2.8 40.2 + - - +
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Residues in contact with VAL 51 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120c ILE* 4.1 22.4 - - + -
521c LMG 4.6 9.2 - - + -
102k BCR 3.5 34.7 - - + +
12z LEU* 3.7 25.1 - - + -
47z TRP* 3.1 43.3 + - + +
48z ILE* 3.7 8.7 - - - +
49z ALA 3.3 0.2 - - - -
50z LEU* 1.3 75.3 - - - +
52z LEU* 1.3 54.6 + - + +
54z VAL 3.5 0.2 + - - -
55z GLY* 2.8 32.1 + - - -
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Residues in contact with LEU 52 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521c LMG 4.5 19.7 - - + -
102k BCR 5.1 13.0 - - + -
48z ILE* 3.3 30.0 + - + +
49z ALA* 3.2 11.5 + - - +
51z VAL* 1.3 78.6 - - + +
53z VAL* 1.3 57.4 + - + +
55z GLY* 3.6 1.5 - - - -
56z VAL* 2.8 40.6 + - + +
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Residues in contact with VAL 53 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8z ALA* 3.9 16.4 - - + -
49z ALA* 2.9 25.3 + - + +
50z LEU* 3.6 12.1 - - + +
51z VAL 3.3 0.2 - - - -
52z LEU* 1.3 73.7 - - + +
54z VAL* 1.3 61.5 + - - +
56z VAL* 3.3 4.4 + - - +
57z LEU* 2.8 52.2 + - + +
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Residues in contact with VAL 54 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15k TYR* 4.7 1.6 - - + +
101k BCR 4.6 2.0 - - + -
102k BCR 4.3 19.3 - - + -
5z PHE* 3.9 21.4 - - + +
8z ALA* 3.8 13.0 - - + +
9z LEU* 3.7 47.1 - - + +
12z LEU* 4.4 9.0 - - + -
50z LEU 2.8 24.2 + - - +
51z VAL* 3.9 3.8 - - - +
53z VAL* 1.3 72.7 - - - +
55z GLY* 1.3 57.8 + - - +
57z LEU* 3.7 4.4 - - - -
58z ASN* 2.9 30.8 + - - +
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Residues in contact with GLY 55 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102k BCR 3.6 32.3 - - - +
51z VAL 2.8 21.5 + - - -
52z LEU* 3.6 3.6 - - - -
53z VAL 3.2 0.2 - - - -
54z VAL* 1.3 74.4 - - - +
56z VAL* 1.3 58.9 + - - +
58z ASN* 3.7 4.9 - - - +
59z PHE* 3.3 26.0 - - - -
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Residues in contact with VAL 56 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52z LEU* 2.8 27.2 + - + +
53z VAL* 3.9 4.7 - - - +
55z GLY* 1.3 69.9 - - - +
57z LEU* 1.3 69.2 + - + +
58z ASN 3.1 5.7 + - - -
59z PHE* 3.1 20.5 + - - +
60z PHE* 3.6 24.1 - - + -
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Residues in contact with LEU 57 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1z FME 4.5 20.2 - - + +
4z LEU* 3.8 28.5 - - + -
5z PHE* 3.7 31.2 - - + -
8z ALA* 4.5 5.2 - - + -
53z VAL* 2.8 37.3 + - + +
54z VAL 3.7 0.4 - - - +
56z VAL* 1.3 78.1 - - + +
58z ASN* 1.3 64.8 + - - +
59z PHE 3.2 0.2 - - - -
60z PHE* 3.2 29.3 + - + +
61z VAL* 3.6 16.6 - - - +
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Residues in contact with ASN 58 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109c PHE* 3.5 27.7 - - - -
112c PHE* 4.5 0.4 - - - -
520c LMG 4.6 0.7 - - - -
15k TYR* 2.6 38.6 + - - +
102k BCR 3.9 15.3 - - + -
5z PHE* 3.9 8.5 - - - -
54z VAL 2.9 17.7 + - - +
55z GLY 3.7 9.9 - - - +
57z LEU* 1.3 77.1 - - - +
59z PHE* 1.3 67.7 + - - +
60z PHE 3.0 1.0 + - - -
61z VAL* 3.3 0.7 + - - -
62z VAL* 3.0 44.2 + - - +
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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