Contacts of the helix formed by residues 9 - 35 (chain X) 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 PHE 9 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q THR* 3.7 27.4 - - + -
8X ASP* 1.3 73.5 - - + +
10X HIS* 1.3 78.6 + + + +
12X LYS* 3.2 3.8 + - - +
13X TYR* 2.8 76.8 + + + -
14X GLY 3.6 0.3 + - - -
17X VAL* 4.6 8.3 - - + -
12Z PRO* 6.4 2.0 - - + -
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Residues in contact with HIS 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408N THR* 3.9 22.8 + - + -
75Q THR* 4.9 4.9 - - + -
76Q ASN* 3.4 33.0 + - + +
77Q GLU* 3.3 34.2 - - + +
80Q THR* 2.8 32.3 + - + -
8X ASP* 3.0 21.6 + - + +
9X PHE* 1.3 89.8 - + + +
11X ASP* 1.3 66.1 + - - +
14X GLY* 3.0 21.7 + - - +
15X ASN* 4.5 1.4 + - - -
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Residues in contact with ASP 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q THR* 5.7 1.4 - - - -
76Q ASN* 2.9 29.1 + - - +
6X ALA 4.7 0.9 - - - +
7X PRO* 3.6 17.5 - - + +
8X ASP* 2.8 47.6 + - - +
10X HIS* 1.3 73.0 - - - +
12X LYS* 1.3 64.4 + - + +
15X ASN* 4.6 9.9 + - - -
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Residues in contact with LYS 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X PRO* 3.7 36.9 + - + +
8X ASP 3.0 13.2 + - - +
9X PHE* 3.6 5.2 - - - +
11X ASP* 1.3 81.5 - - - +
13X TYR* 1.3 96.8 + - + +
15X ASN* 4.7 4.5 + - - +
16X ALA* 5.2 1.9 + - - +
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Residues in contact with TYR 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X PHE* 2.8 61.9 + + + +
12X LYS* 1.3 102.6 + - + +
14X GLY* 1.3 64.4 + - - +
15X ASN 3.2 2.5 - - - -
16X ALA* 2.8 24.3 + - + +
17X VAL* 2.9 20.8 + - + +
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Residues in contact with GLY 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q LYS* 3.4 17.8 - - - +
80Q THR* 3.8 19.9 + - - -
9X PHE* 3.6 2.8 + - - -
10X HIS* 3.0 22.9 + - - +
12X LYS 3.5 0.6 - - - -
13X TYR* 1.3 75.5 - - - +
15X ASN* 1.3 56.6 + - - +
17X VAL* 3.4 3.4 + - - +
18X LEU* 3.0 29.3 + - - +
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Residues in contact with ASN 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q ASN* 5.4 2.0 - - - +
79Q LYS* 3.0 39.3 + - - +
10X HIS 5.1 1.0 + - - -
11X ASP 4.6 11.5 + - - -
12X LYS 4.7 3.4 + - - +
13X TYR 3.2 0.8 - - - -
14X GLY* 1.3 75.9 - - - +
16X ALA* 1.3 61.4 + - - +
18X LEU* 3.6 8.0 - - - +
19X ALA* 3.2 24.4 + - - +
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Residues in contact with ALA 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X LYS 5.2 1.3 + - - +
13X TYR* 2.8 24.5 + - + +
15X ASN* 1.3 71.5 - - - +
17X VAL* 1.3 61.4 + - + +
19X ALA* 3.1 3.6 + - - +
20X SER* 2.8 37.3 + - - +
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Residues in contact with VAL 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q THR* 3.6 21.5 - - + +
83Q GLY* 3.8 2.5 - - - -
84Q ALA* 3.6 29.8 - - + +
87Q PHE* 6.4 0.2 - - + -
9X PHE* 4.6 15.7 - - + -
13X TYR* 2.9 26.8 + - + +
14X GLY 3.7 7.2 - - - +
16X ALA* 1.3 76.3 - - + +
18X LEU* 1.3 64.3 + - - +
20X SER* 3.9 4.9 - - - -
21X GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q TRP* 4.0 28.3 - - + -
79Q LYS* 3.7 20.2 + - + +
82Q VAL* 3.8 20.0 - - + -
83Q GLY* 3.7 24.7 - - - +
86Q MET* 5.7 0.2 - - - -
14X GLY 3.0 19.4 + - - +
15X ASN* 3.6 9.4 - - - +
16X ALA 3.2 0.2 - - - -
17X VAL* 1.3 76.4 - - - +
19X ALA* 1.3 59.5 + - + +
22X ALA* 3.0 36.3 + - + +
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Residues in contact with ALA 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X ASN 3.2 12.7 + - - +
16X ALA* 3.1 4.2 + - - +
18X LEU* 1.3 79.0 - - + +
20X SER* 1.3 67.6 + - - +
22X ALA* 3.6 4.3 - - - +
23X THR* 2.8 31.2 + - - +
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Residues in contact with SER 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q PHE* 6.0 0.2 - - - -
16X ALA* 2.8 29.5 + - - +
17X VAL* 3.6 4.7 + - - -
19X ALA* 1.3 72.9 - - - +
21X GLY* 1.3 63.6 + - - +
23X THR* 3.6 5.9 - - - +
24X PHE* 2.9 26.8 + - - +
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Residues in contact with GLY 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Q GLY 3.9 12.6 - - - -
86Q MET* 4.1 9.4 - - - +
87Q PHE* 4.1 17.7 + - - -
17X VAL 2.9 17.1 + - - -
20X SER* 1.3 80.3 + - - +
22X ALA* 1.3 62.0 + - - +
24X PHE* 3.2 4.5 + - - +
25X CYS* 3.0 24.8 + - - +
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Residues in contact with ALA 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Q GLY 4.7 0.4 + - - -
86Q MET* 3.8 29.6 - - + +
18X LEU* 3.0 24.4 + - + +
19X ALA* 3.6 5.6 - - - +
21X GLY* 1.3 75.5 - - - +
23X THR* 1.3 62.5 + - - +
25X CYS* 3.6 1.7 + - - +
26X VAL* 3.0 30.9 + - + +
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Residues in contact with THR 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X ALA* 2.8 22.8 + - - +
20X SER* 3.6 6.3 - - - -
22X ALA* 1.3 75.4 - - - +
24X PHE* 1.3 69.1 + - - +
25X CYS 3.2 0.3 + - - -
26X VAL* 3.2 8.5 + - - +
27X ALA* 3.1 22.7 + - + +
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Residues in contact with PHE 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q PHE* 3.4 55.4 - + + -
90Q GLY* 3.7 3.8 - - - -
91Q PHE* 3.5 21.5 - + + -
94Q LEU* 4.6 14.1 - - + -
20X SER 2.9 18.2 + - - +
21X GLY* 3.5 3.1 - - - +
23X THR* 1.3 79.0 - - - +
25X CYS* 1.3 66.6 + - - +
27X ALA* 3.3 5.0 + - + +
28X VAL* 3.0 48.5 + - + +
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Residues in contact with CYS 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q MET* 3.1 46.4 - - + +
89Q ILE* 3.8 24.7 - - - -
90Q GLY* 3.8 11.4 - - - -
21X GLY 3.0 12.1 + - - +
22X ALA 3.7 5.2 - - - +
24X PHE* 1.3 78.9 - - - +
26X VAL* 1.3 67.9 + - - +
27X ALA 3.1 0.2 + - - -
28X VAL* 3.4 0.7 + - - +
29X TRP* 3.1 34.1 + - - -
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Residues in contact with VAL 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q MET* 5.0 8.1 - - + -
22X ALA* 3.0 17.9 - - + +
23X THR* 3.2 7.7 + - - +
25X CYS* 1.3 77.9 - - + +
27X ALA* 1.3 56.0 + - - +
29X TRP* 4.0 3.5 - - - +
30X VAL* 3.0 43.4 + - + +
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Residues in contact with ALA 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X THR* 3.1 14.8 + - + +
24X PHE* 3.7 10.1 - - + +
25X CYS 3.2 0.2 - - - -
26X VAL* 1.3 74.5 - - - +
28X VAL* 1.3 69.4 + - + +
29X TRP 3.1 0.2 + - - -
30X VAL* 3.1 5.0 + - - +
31X TYR* 2.8 26.1 + - - +
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Residues in contact with VAL 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q GLY 4.0 8.5 - - - +
93Q ALA* 3.7 16.2 - - + -
94Q LEU* 3.4 33.2 - - + -
97Q ILE* 4.0 7.6 - - + -
24X PHE* 3.0 50.2 + - + +
25X CYS 4.1 1.6 - - - +
27X ALA* 1.3 75.4 - - + +
29X TRP* 1.3 57.9 + - - +
31X TYR* 3.6 5.8 - - + +
32X MET* 2.8 32.2 + - - +
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Residues in contact with TRP 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423N MET* 4.6 13.5 - - + -
456N MET* 4.3 21.1 - - + -
460N ILE* 4.3 26.7 - - + -
89Q ILE* 2.8 32.5 + - + +
90Q GLY* 3.8 9.4 - - - -
92Q THR* 4.8 0.7 - - - -
93Q ALA* 3.4 21.0 - - + +
96Q LEU* 3.9 24.9 - - + -
25X CYS* 3.1 33.8 + - - +
26X VAL* 4.0 4.5 - - - +
27X ALA 3.1 0.8 - - - -
28X VAL* 1.3 75.6 - - - +
30X VAL* 1.3 62.5 + - + +
32X MET* 3.2 26.9 + - + +
33X ALA* 2.8 34.9 + - + +
40X TRP* 6.0 0.7 - + - -
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Residues in contact with VAL 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X VAL* 3.0 35.3 + - + +
27X ALA* 3.7 3.1 - - - +
29X TRP* 1.3 76.2 - - + +
31X TYR* 1.3 67.0 + - - +
33X ALA* 3.3 4.4 + - - +
34X THR* 2.8 38.6 + - + +
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Residues in contact with TYR 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q ILE* 3.7 28.9 - - + -
27X ALA 2.8 16.6 + - - +
28X VAL* 3.6 6.3 - - + +
30X VAL* 1.3 78.1 - - - +
32X MET* 1.3 63.7 + - - +
34X THR* 2.9 2.0 + - - -
35X GLN* 2.7 72.4 + - + +
36X ILE* 4.2 20.1 - - + +
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Residues in contact with MET 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456N MET* 4.3 20.0 - - + -
93Q ALA* 4.0 9.4 - - + +
96Q LEU* 3.6 36.6 - - + -
97Q ILE* 3.5 28.0 - - + -
28X VAL 2.8 21.7 + - - +
29X TRP* 3.7 29.2 - - + +
31X TYR* 1.3 79.9 - - - +
33X ALA* 1.3 84.9 + - + +
34X THR 3.3 0.2 + - - -
36X ILE* 3.1 34.4 - - + +
38X ILE* 3.4 8.1 - - + +
40X TRP* 4.6 1.1 - - + -
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Residues in contact with ALA 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X TRP* 2.8 22.6 + - + +
30X VAL* 3.9 5.6 - - - +
31X TYR 3.1 0.2 - - - -
32X MET* 1.3 83.3 - - + +
34X THR* 1.3 67.1 + - + +
36X ILE 5.3 1.1 - - - +
38X ILE* 5.0 2.3 - - - +
40X TRP* 2.7 47.9 + - + -
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Residues in contact with THR 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X VAL* 2.8 29.8 + - + +
31X TYR* 2.9 1.3 + - - -
33X ALA* 1.3 90.8 - - + +
35X GLN* 1.3 77.8 + - - +
36X ILE 3.6 8.9 - - - +
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Residues in contact with GLN 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X TYR* 2.7 61.8 + - + +
34X THR* 1.3 86.9 + - - +
36X ILE* 1.3 62.8 + - - +
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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
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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