Contacts of the helix formed by residues 9 - 37 (chain R) in PDB entry 2QJK
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 GLY 9 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Q ARG* 6.0 0.6 - - - +
10R THR* 1.3 59.9 + - - -
11R ARG* 3.2 20.8 + - - +
12R ARG* 3.6 41.7 + - - +
13R ASP* 3.8 5.4 - - - +
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Residues in contact with THR 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R GLY* 1.3 71.3 - - - -
11R ARG* 1.3 60.9 + - - +
12R ARG 3.6 1.1 - - - -
13R ASP* 3.7 16.4 + - + +
14R PHE* 3.0 34.3 - - + +
17R TYR* 6.2 0.7 - - + -
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Residues in contact with ARG 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Q ARG* 5.6 6.7 - - - +
9R GLY* 3.2 13.8 - - - +
10R THR* 1.3 82.7 - - - +
12R ARG* 1.3 62.9 + - - +
14R PHE* 3.6 16.6 - - - +
15R LEU* 3.6 7.4 + - - +
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Residues in contact with ARG 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250Q ARG* 2.9 55.4 - - - +
9R GLY* 3.6 31.5 + - - +
11R ARG* 1.3 77.2 - - - +
13R ASP* 1.3 77.0 + - + +
14R PHE 3.2 0.4 - - - -
15R LEU* 3.1 6.7 + - - +
16R TYR* 2.9 46.7 + - + -
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Residues in contact with ASP 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R GLY 3.8 6.1 - - - +
10R THR* 3.7 26.5 + - + +
11R ARG 3.4 0.2 - - - -
12R ARG* 1.3 82.9 - - + +
14R PHE* 1.3 65.9 + - - +
16R TYR* 3.3 13.8 + - - +
17R TYR* 3.0 58.4 + - - -
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Residues in contact with PHE 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243Q LEU* 6.3 0.7 - - + -
10R THR* 3.0 30.5 + - + +
11R ARG* 3.6 9.2 - - - +
12R ARG 3.2 0.2 - - - -
13R ASP* 1.3 76.3 - - - +
15R LEU* 1.3 72.0 + - + +
17R TYR* 2.9 9.1 + - + +
18R ALA* 2.7 53.4 + - + -
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Residues in contact with LEU 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243Q LEU* 3.9 29.6 - - + +
246Q LEU* 3.9 24.5 - - + -
247Q THR* 3.6 39.3 - - - +
250Q ARG* 4.7 16.2 - - + -
11R ARG 3.6 8.2 + - - +
12R ARG* 3.1 9.3 + - - +
14R PHE* 1.3 91.1 - - + +
16R TYR* 1.3 56.7 + - + +
18R ALA* 2.9 5.5 + - - +
19R THR* 2.7 37.7 + - - +
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Residues in contact with TYR 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250P ILE* 6.0 1.3 - - + -
247Q THR* 4.1 27.1 + - + -
250Q ARG* 4.3 19.2 + - - -
251Q LEU* 4.6 20.8 - - + +
12R ARG* 2.9 46.7 + - + +
13R ASP* 3.5 18.4 - - - +
15R LEU* 1.3 80.3 - - + +
17R TYR* 1.3 59.8 + - + +
19R THR* 3.7 7.2 - - - +
20R ALA* 3.1 28.4 + - - +
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Residues in contact with TYR 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R THR* 6.2 0.7 - - + -
13R ASP* 3.0 50.9 + - - +
14R PHE* 2.9 11.6 + - + +
16R TYR* 1.3 76.2 - - + +
18R ALA* 1.3 65.0 + - - +
19R THR 3.2 1.3 - - - -
20R ALA* 4.3 5.6 - - + +
21R GLY* 3.3 18.1 + - - -
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Residues in contact with ALA 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243Q LEU* 3.7 23.2 - - + +
14R PHE* 2.7 39.9 + - + +
15R LEU* 3.5 9.0 - - - +
17R TYR* 1.3 73.8 - - - +
19R THR* 1.3 62.9 + - - +
21R GLY* 3.5 2.0 + - - -
22R ALA* 3.2 16.8 + - - +
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Residues in contact with THR 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240Q LEU* 4.4 4.7 - - + +
243Q LEU* 3.4 27.0 - - - +
244Q LEU* 4.1 21.3 + - + +
247Q THR* 3.3 26.6 + - + +
15R LEU* 2.7 15.0 + - - +
16R TYR* 3.7 8.3 - - - +
18R ALA* 1.3 73.9 - - - +
20R ALA* 1.3 70.8 + - + +
21R GLY 2.7 5.6 + - - -
22R ALA* 2.8 14.7 + - - +
23R GLY* 3.0 10.2 + - - -
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Residues in contact with ALA 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R TYR 3.1 14.9 + - - +
17R TYR* 4.5 7.0 - - + +
19R THR* 1.3 84.5 - - + +
21R GLY* 1.3 60.7 + - - +
23R GLY* 3.3 3.4 + - - +
24R ALA* 3.0 24.1 + - - +
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Residues in contact with GLY 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R TYR 3.3 13.2 + - - -
18R ALA* 3.7 5.2 - - - -
19R THR 2.7 2.6 + - - -
20R ALA* 1.3 76.1 - - - +
22R ALA* 1.3 65.1 + - - -
23R GLY 3.2 0.3 + - - -
24R ALA* 3.2 8.5 + - - +
25R VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 5.1 8.4 - - + +
239Q VAL* 5.3 4.5 - - + -
240Q LEU* 3.9 26.8 - - + +
243Q LEU* 4.4 10.1 - - + -
18R ALA 3.2 11.1 + - - +
19R THR 2.8 10.2 + - - +
21R GLY* 1.3 70.3 - - - -
23R GLY* 1.3 68.2 + - - +
25R VAL* 3.1 12.7 + - - +
26R ALA* 3.0 21.0 + - - +
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Residues in contact with GLY 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240Q LEU* 4.2 15.5 - - - +
19R THR 3.0 11.7 + - - -
20R ALA* 3.6 5.4 - - - -
21R GLY 3.1 0.2 - - - -
22R ALA* 1.3 79.7 - - - +
24R ALA* 1.3 65.4 + - - +
26R ALA* 3.0 3.2 + - - +
27R THR* 2.9 25.7 + - - -
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Residues in contact with ALA 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R ALA 3.0 12.7 + - - +
21R GLY* 3.5 9.9 - - - +
23R GLY* 1.3 72.8 - - - +
25R VAL* 1.3 65.2 + - + +
27R THR* 3.1 11.2 + - - -
28R GLY* 3.0 20.3 + - - -
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Residues in contact with VAL 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 3.1 33.2 - - + -
21R GLY 3.0 19.2 + - - +
22R ALA* 3.2 14.1 - - - +
23R GLY 3.1 0.2 + - - -
24R ALA* 1.3 77.6 - - + +
26R ALA* 1.3 66.8 + - - +
28R GLY* 3.2 1.9 + - - -
29R ALA* 3.0 16.5 + - - +
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Residues in contact with ALA 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 4.1 22.9 - - + -
237Q LEU* 6.2 1.8 - - + -
240Q LEU* 4.8 14.4 - - + -
22R ALA 3.0 6.6 + - - +
23R GLY* 3.0 9.0 + - - +
25R VAL* 1.3 76.4 - - - +
27R THR* 1.3 58.8 + - - +
29R ALA* 2.5 35.5 + - - +
30R ALA* 3.0 10.8 + - - +
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Residues in contact with THR 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R GLY 2.9 17.2 + - - -
24R ALA* 3.2 14.2 - - - +
26R ALA* 1.3 74.3 - - - +
28R GLY* 1.3 63.1 + - - +
30R ALA* 3.2 8.8 - - - +
31R VAL* 3.1 35.3 + - + +
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Residues in contact with GLY 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R ALA 3.0 12.9 + - - -
25R VAL 3.7 2.7 - - - -
26R ALA 2.8 1.4 + - - -
27R THR* 1.3 72.5 - - - +
29R ALA* 1.3 58.1 + - - +
30R ALA 2.9 5.7 + - - -
31R VAL* 3.0 8.9 + - - +
32R TRP* 2.8 32.8 + - - +
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Residues in contact with ALA 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 3.8 25.1 - - + -
25R VAL 3.0 12.4 + - - +
26R ALA 2.5 16.9 + - - +
28R GLY* 1.3 69.6 - - - +
30R ALA* 1.3 54.1 + - - -
32R TRP* 4.5 2.9 - - - +
33R PRO* 2.9 24.5 - - - +
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Residues in contact with ALA 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R ALA 3.0 7.4 + - - +
27R THR* 3.2 13.2 - - - +
29R ALA* 1.3 76.9 - - - +
31R VAL* 1.3 65.1 + - + +
33R PRO* 2.8 24.9 - - - +
34R LEU* 3.4 17.5 + - + +
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Residues in contact with VAL 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R THR* 3.2 24.9 - - + +
28R GLY* 3.5 9.4 - - - +
30R ALA* 1.3 76.3 - - + +
32R TRP* 1.3 69.0 + - - +
34R LEU* 3.0 23.4 + - + +
35R ILE* 3.1 34.9 + - + +
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Residues in contact with TRP 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R GLY 2.8 17.5 + - - +
29R ALA* 4.5 3.4 - - - +
31R VAL* 1.3 73.4 - - - +
33R PRO* 1.4 63.4 - - + +
35R ILE* 2.6 53.3 + - + +
36R ASN* 2.7 54.8 + - + +
39R ASN* 4.3 6.5 - - - -
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Residues in contact with PRO 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ASN 4.5 5.4 - - - +
89P GLY* 6.0 4.3 - - - -
93P LEU* 4.8 12.0 - - + +
29R ALA 2.9 23.8 - - - +
30R ALA* 2.8 26.5 - - - +
32R TRP* 1.4 91.6 - - + +
34R LEU* 1.3 60.5 + - + +
35R ILE 3.0 0.2 - - - -
36R ASN* 3.8 9.2 - - + +
37R GLN* 3.1 26.5 + - - +
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Residues in contact with LEU 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P VAL* 4.0 29.8 - - + -
61P THR* 5.1 2.0 - - + -
64P VAL* 3.9 25.6 - - + +
93P LEU* 4.6 17.5 - - + -
30R ALA* 3.5 17.9 - - + +
31R VAL* 3.0 18.4 + - + +
33R PRO* 1.3 78.5 - - + +
35R ILE* 1.3 60.2 + - + +
37R GLN* 3.0 29.6 + - - +
38R MET* 5.1 0.7 - - - +
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Residues in contact with ILE 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M TRP* 3.1 46.8 + - + +
31R VAL* 3.3 33.0 - - + +
32R TRP* 2.6 28.1 + - + +
34R LEU* 1.3 79.0 - - + +
36R ASN* 1.3 66.3 + - - +
37R GLN 3.1 1.3 - - - -
38R MET* 3.0 14.2 + - - +
39R ASN* 5.8 0.4 - - - +
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Residues in contact with ASN 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ASN* 3.0 27.4 + - + +
32R TRP* 2.7 53.4 + - + +
33R PRO* 4.2 7.2 - - + -
35R ILE* 1.3 74.2 - - - +
37R GLN* 1.3 55.6 + - - +
38R MET 2.9 0.2 - - - -
39R ASN* 2.6 61.4 + - - +
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Residues in contact with GLN 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P VAL* 3.6 25.7 - - + +
67P MET* 3.7 15.8 - - - +
68P HIS* 2.7 39.0 + - - -
87P VAL* 3.6 22.9 - - + +
88P ASN* 3.5 23.9 + - - +
93P LEU* 4.1 9.6 - - + -
33R PRO 3.1 15.0 + - - +
34R LEU* 3.0 30.6 + - - +
36R ASN* 1.3 75.9 - - - +
38R MET* 1.3 89.3 + - - +
39R ASN 3.5 7.8 - - - +
41R SER* 6.1 0.2 - - - -
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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