Contacts of the helix formed by residues 41 - 66 (chain P) in PDB entry 1OCR
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 THR 41 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P SER* 3.4 14.6 + - - -
40P MET* 1.3 76.1 + - - +
42P LEU* 1.3 65.1 + - - +
44P MET* 3.1 7.3 + - + +
45P ILE* 2.8 43.6 + - + +
45W TYR* 4.3 18.9 + - + -
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Residues in contact with LEU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU* 3.8 19.8 - - + +
29P SER* 3.8 11.9 - - - +
30P GLY* 3.6 10.8 - - - +
33P MET* 4.1 26.9 - - + +
39P SER* 4.9 2.4 + - - -
40P MET 3.4 0.2 - - - -
41P THR* 1.3 75.7 - - - +
43P LEU* 1.3 64.9 + - - +
45P ILE* 3.0 12.4 + - + +
46P GLY* 2.8 21.5 + - - -
42W GLY* 3.8 19.7 - - - +
45W TYR* 3.5 26.8 - - + -
46W SER* 3.5 30.3 - - - +
49W CYS* 4.6 7.9 - - + -
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Residues in contact with LEU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU 4.2 2.7 - - - -
27P MET* 3.9 25.8 - - + +
30P GLY* 3.3 23.8 + - - +
31P LEU* 4.1 25.8 - - + -
34P TRP* 4.7 10.8 - - + -
40P MET* 3.2 27.4 + - + +
42P LEU* 1.3 78.7 - - - +
44P MET* 1.3 64.5 + - + +
46P GLY* 3.3 0.9 + - - -
47P LEU* 2.9 46.4 + - + +
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Residues in contact with MET 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P MET* 2.8 42.6 + - + +
41P THR* 3.3 7.4 - - + +
43P LEU* 1.3 84.6 - - + +
45P ILE* 1.3 67.4 + - + +
47P LEU* 3.4 26.7 + - + +
48P THR* 2.9 26.5 + - - -
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Residues in contact with ILE 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU* 3.8 20.4 - - + -
41P THR* 2.8 36.4 + - + +
42P LEU* 3.5 18.4 - - + +
44P MET* 1.3 75.2 - - + +
46P GLY* 1.3 64.6 + - - +
48P THR* 3.0 8.9 + - - -
49P THR* 3.0 26.0 + - + +
38W LEU* 4.2 25.1 - - + +
42W GLY* 4.3 11.0 - - - -
45W TYR* 4.5 7.9 - - + -
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Residues in contact with GLY 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P SER* 4.4 1.1 - - - -
26P LEU* 3.4 27.5 - - - +
27P MET* 3.7 15.2 - - - +
42P LEU 2.8 12.0 + - - -
43P LEU 3.6 3.8 - - - -
45P ILE* 1.3 77.4 - - - +
47P LEU* 1.3 61.9 + - - +
49P THR* 3.0 17.8 + - - -
50P ASN* 3.0 12.8 + - - +
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Residues in contact with LEU 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P MET* 4.0 16.5 - - - +
43P LEU* 2.9 38.7 + - + +
44P MET* 3.8 30.1 - - + +
45P ILE 3.3 0.2 - - - -
46P GLY* 1.3 72.7 - - - +
48P THR* 1.3 62.6 + - - +
50P ASN* 3.4 7.7 + - + +
51P MET* 3.1 40.3 + - + +
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Residues in contact with THR 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P MET* 2.9 14.9 + - - +
45P ILE* 3.0 11.4 + - - -
47P LEU* 1.3 73.3 - - - +
49P THR* 1.3 66.6 + - - +
50P ASN 3.1 0.3 + - - -
51P MET* 3.1 9.1 + - - +
52P LEU* 3.0 30.5 + - + +
38W LEU* 4.2 22.0 - - + -
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Residues in contact with THR 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P THR* 4.4 0.7 - - - +
23P SER* 3.1 15.6 + - - -
26P LEU* 3.7 15.7 - - + +
45P ILE* 3.0 12.3 + - + +
46P GLY 3.0 14.6 + - - -
48P THR* 1.3 75.0 - - - +
50P ASN* 1.3 52.8 + - - +
52P LEU* 3.5 9.7 - - + +
53P THR* 2.7 37.4 + - - -
35W THR* 4.5 2.2 - - - +
38W LEU* 3.5 37.0 - - + -
39W CYS* 3.7 26.5 - - - +
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Residues in contact with ASN 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P GLY* 5.2 2.4 - - - +
23P SER* 3.6 17.1 - - - -
27P MET* 3.4 31.4 - - - +
46P GLY 3.0 12.8 + - - +
47P LEU* 3.4 13.1 + - + +
49P THR* 1.3 74.8 + - - +
51P MET* 1.3 63.8 + - - +
53P THR* 3.2 4.9 + - - -
54P MET* 2.9 59.2 + - - +
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Residues in contact with MET 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P LEU* 3.1 29.2 - - + +
48P THR* 3.1 6.8 + - - +
50P ASN* 1.3 80.1 - - - +
52P LEU* 1.3 58.7 + - + +
54P MET* 3.3 23.6 + - - +
55P TYR* 2.8 32.7 + - - +
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Residues in contact with LEU 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P THR* 3.0 25.1 + - + +
49P THR* 3.5 12.1 - - - +
51P MET* 1.3 79.0 - - + +
53P THR* 1.3 62.7 + - - +
55P TYR* 3.4 7.4 + - + +
56P GLN* 2.8 34.1 + - - +
31W LEU* 4.1 25.4 - - + -
34W VAL* 4.6 7.2 - - + -
35W THR* 3.7 29.2 - - + +
38W LEU* 4.1 26.7 - - + -
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Residues in contact with THR 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P TRP* 3.5 36.4 - - + +
19P THR* 2.7 25.7 - - + +
20P GLY* 3.7 14.6 - - - +
23P SER* 3.7 3.3 + - - -
49P THR 2.7 22.0 + - - -
50P ASN* 3.5 7.4 - - - -
52P LEU* 1.3 74.7 - - - +
54P MET* 1.3 61.8 + - + +
56P GLN* 3.3 5.5 + - - +
57P TRP* 2.8 43.0 + - + +
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Residues in contact with MET 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P ASN* 2.9 43.2 + - - +
51P MET* 3.9 23.8 - - - +
53P THR* 1.3 76.8 - - + +
55P TYR* 1.3 63.4 + - - +
57P TRP* 4.5 4.5 - - - -
58P TRP* 3.1 66.1 + - + +
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Residues in contact with TYR 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P MET 2.8 19.4 + - - +
52P LEU* 3.7 8.5 - - + +
54P MET* 1.3 78.2 - - - +
56P GLN* 1.3 71.4 + - + +
58P TRP* 3.8 2.7 - - - +
59P ARG* 2.9 52.0 + - + +
31W LEU* 3.9 28.0 - - + +
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Residues in contact with GLN 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P TRP* 3.0 46.6 - - + -
52P LEU* 2.8 31.4 + - - +
53P THR 4.1 1.1 - - - +
55P TYR* 1.3 86.5 - - + +
57P TRP* 1.3 66.3 + - - +
59P ARG* 3.5 22.3 + - - +
60P ASP* 3.0 31.4 + - - +
28W ASP 4.5 0.7 - - - +
31W LEU* 3.3 27.1 - - + +
32W TYR 3.6 4.3 + - - -
35W THR* 3.0 24.0 + - - +
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Residues in contact with TRP 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ARG* 3.4 28.2 - - + +
97N MET* 3.8 40.8 - - + -
100N MET* 3.8 35.7 - - + -
16P TRP* 3.7 33.3 - + + -
17P PRO* 3.9 23.1 - - + -
53P THR* 2.8 31.2 + - + +
54P MET* 4.0 4.9 - - - +
56P GLN* 1.3 74.5 - - - +
58P TRP* 1.3 75.7 + + + +
60P ASP* 3.2 4.2 + - - +
61P VAL* 3.1 29.3 + - + +
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Residues in contact with TRP 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P MET* 3.1 64.7 + - + +
55P TYR* 4.2 2.0 - - - +
57P TRP* 1.3 89.0 - + + +
59P ARG* 1.3 64.8 + - - +
61P VAL* 3.3 18.8 + - + +
62P ILE* 3.1 31.3 + - + +
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Residues in contact with ARG 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P TRP* 4.1 11.3 - - - -
55P TYR* 2.9 44.9 + - + +
56P GLN* 3.5 22.4 + - - +
58P TRP* 1.3 75.1 - - - +
60P ASP* 1.3 88.6 + - - +
62P ILE* 3.1 13.4 + - - +
63P ARG* 3.0 52.1 + - + +
21W HIS* 3.2 29.7 + - - +
28W ASP* 3.5 22.8 + - - +
31W LEU* 4.1 15.0 - - - +
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Residues in contact with ASP 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ARG* 4.0 17.2 + - - +
14P SER* 5.0 1.0 + - - -
16P TRP* 2.8 29.6 + - - -
56P GLN 3.0 8.6 + - - -
57P TRP* 3.5 8.1 - - - +
59P ARG* 1.3 104.2 + - - +
61P VAL* 1.3 53.4 + - - +
63P ARG* 2.9 12.8 + - - +
64P GLU* 2.7 39.6 + - - +
20W VAL* 4.1 12.2 - - + +
21W HIS* 3.3 19.2 + - - +
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Residues in contact with VAL 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ARG* 3.6 21.3 - - - +
57P TRP* 3.1 26.7 + - + +
58P TRP* 3.7 20.9 - - + +
59P ARG 3.3 0.2 - - - -
60P ASP* 1.3 74.3 - - - +
62P ILE* 1.3 55.1 + - + +
64P GLU* 3.4 9.3 + - - +
65P SER* 2.7 33.4 + - - +
71P HIS* 4.1 20.5 - - + +
79P LEU* 5.9 3.4 - - + -
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Residues in contact with ILE 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P TRP* 3.1 17.1 + - + +
59P ARG* 3.1 11.6 + - - +
60P ASP 3.1 0.6 - - - -
61P VAL* 1.3 76.8 - - + +
63P ARG* 1.3 60.7 + - + +
65P SER* 3.0 5.9 + - - -
66P THR* 2.8 35.7 + - - -
67P PHE* 3.6 9.8 + - + -
217P VAL* 5.3 6.1 - - + -
221P ARG* 3.5 41.3 - - + +
226P HIS* 3.7 29.2 - - + +
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Residues in contact with ARG 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ARG* 3.0 52.0 + - + +
60P ASP* 2.9 16.3 + - - +
62P ILE* 1.3 75.7 - - + +
64P GLU* 1.3 52.2 + - - +
67P PHE* 3.1 31.9 - - + +
68P GLN* 2.8 36.5 + - - +
12W PHE* 3.4 27.3 - - + -
20W VAL* 2.7 45.5 + - + -
24W GLY* 3.7 10.1 - - - +
28W ASP* 2.8 40.2 + - - -
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Residues in contact with GLU 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ARG* 2.8 46.3 + - - -
9P HIS* 3.5 32.4 + - + +
11P VAL* 4.2 6.1 - - - +
12P ASN 5.1 1.0 + - - -
60P ASP 2.7 22.1 + - - +
61P VAL* 3.7 12.9 - - - +
63P ARG* 1.3 72.9 - - - +
65P SER* 1.3 57.2 + - - +
68P GLN* 3.6 19.5 - - - +
69P GLY 3.5 1.9 + - - -
70P HIS* 2.9 32.8 + - + +
71P HIS* 4.8 4.0 + - - +
20W VAL* 3.6 20.9 - - + +
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Residues in contact with SER 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P VAL* 2.7 22.7 + - - +
62P ILE* 3.0 7.8 + - - -
64P GLU* 1.3 78.8 - - - +
66P THR* 1.3 70.7 + - - +
67P PHE 3.4 0.4 - - - -
69P GLY* 3.1 23.8 + - - -
70P HIS 4.2 1.3 - - - +
71P HIS* 3.3 40.0 + - - +
221P ARG* 4.7 3.1 + - - -
231P HIS* 5.4 5.2 - - - -
14S THR* 4.8 0.2 - - - +
17S GLU* 4.5 7.6 - - - +
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Residues in contact with THR 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P ILE* 2.8 18.3 + - - -
65P SER* 1.3 79.3 + - - +
67P PHE* 1.3 81.0 + - + +
221P ARG* 2.9 29.1 + - - -
226P HIS* 3.9 29.1 + - + +
12S GLN* 5.0 1.9 - - - +
14S THR* 4.0 2.9 - - - +
5W VAL* 4.1 13.9 - - + -
9W GLN* 3.3 21.7 + - - +
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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
------------------------------------------------------------
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