Contacts of the helix formed by residues 12 - 36 (chain U) in PDB entry 1JJ2
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 12 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U MET* 1.3 75.7 - - - +
13U PRO* 1.3 73.8 - - - +
14U ALA* 3.4 14.4 + - + +
15U GLU* 2.6 72.3 + - + +
16U ARG* 3.1 11.2 + - - +
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Residues in contact with PRO 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U MET 4.4 0.9 - - - +
12U THR* 1.3 91.9 - - - +
14U ALA* 1.3 58.5 + - - +
16U ARG* 3.5 14.9 + - - +
17U GLU* 3.3 31.7 + - - +
60U GLN* 5.1 0.2 - - - +
63U GLU* 6.0 0.4 - - + -
65U ASP* 3.5 40.1 - - + +
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Residues in contact with ALA 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U THR* 3.0 13.2 + - + +
13U PRO* 1.3 78.5 - - - +
15U GLU* 1.3 61.1 + - - +
17U GLU* 3.6 9.3 + - - +
18U ALA* 3.1 26.7 + - - +
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Residues in contact with GLU 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U ASP 4.4 2.9 - - - +
11U MET* 3.6 23.8 - - + +
12U THR* 2.6 59.0 + - + +
14U ALA* 1.3 71.4 - - - +
16U ARG* 1.3 59.5 + - - +
18U ALA* 3.7 6.3 - - - +
19U GLU* 2.8 30.7 + - - +
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Residues in contact with ARG 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ILE* 3.2 22.7 + - + +
9U ARG* 3.6 11.9 + - - +
11U MET* 3.3 39.1 + - + -
12U THR 3.1 7.7 + - - +
13U PRO* 3.7 19.0 - - - +
15U GLU* 1.3 75.8 - - - +
17U GLU* 1.3 53.3 + - - +
19U GLU* 3.2 2.2 + - - +
20U LEU* 2.5 37.6 + - - +
56U ILE* 3.8 16.6 - - + +
59U ILE* 3.9 7.8 - - - +
60U GLN* 4.1 20.3 - - + +
63U GLU* 3.3 40.9 + - - +
65U ASP 2.7 40.6 + - - -
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Residues in contact with GLU 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U PRO* 3.3 21.6 + - - +
14U ALA* 3.9 10.0 - - - +
16U ARG* 1.3 77.2 - - - +
18U ALA* 1.3 57.4 + - - +
20U LEU* 3.3 10.6 - - + +
21U ASP* 2.9 41.1 + - - +
60U GLN* 3.7 19.1 - - - +
65U ASP* 5.2 8.5 - - - +
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Residues in contact with ALA 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U ALA 3.1 18.4 + - - +
15U GLU* 3.8 7.4 - - - +
17U GLU* 1.3 77.7 - - - +
19U GLU* 1.3 58.6 + - - +
21U ASP* 3.7 5.2 + - - +
22U ASP* 2.7 35.9 + - - +
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Residues in contact with GLU 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U LEU* 4.0 13.7 - - + +
11U MET* 4.0 25.3 - - + +
15U GLU 2.8 20.0 + - - +
16U ARG* 3.5 4.0 - - - +
18U ALA* 1.3 73.8 - - - +
20U LEU* 1.3 59.4 + - - +
22U ASP* 3.2 12.9 + - - +
23U LEU* 3.0 44.1 + - + +
56U ILE* 3.6 18.6 - - + -
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Residues in contact with LEU 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U ARG 2.5 21.0 + - - +
17U GLU* 3.2 9.6 + - + +
19U GLU* 1.3 68.8 - - - +
21U ASP* 1.3 65.5 + - - +
22U ASP 2.9 3.4 - - - -
23U LEU* 2.9 15.6 + - - +
24U LYS* 3.0 30.7 + - - +
53U ILE* 3.7 37.2 - - + +
56U ILE* 4.0 20.9 - - + -
57U LYS* 4.0 18.2 - - + +
60U GLN* 3.2 30.7 - - - +
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Residues in contact with ASP 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U GLU* 2.9 25.4 + - - +
18U ALA* 4.2 5.4 - - - +
20U LEU* 1.3 76.6 - - - +
22U ASP* 1.3 59.8 + - - +
24U LYS* 4.0 21.2 + - - +
25U THR* 3.0 26.7 + - - -
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Residues in contact with ASP 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U ALA* 2.7 27.2 + - - +
19U GLU* 3.3 18.3 - - - +
20U LEU 2.9 0.6 - - - -
21U ASP* 1.3 77.6 - - - +
23U LEU* 1.3 65.3 + - + +
25U THR* 3.3 8.4 + - - -
26U GLU* 3.1 20.3 + - - +
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Residues in contact with LEU 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U LEU* 4.3 4.5 - - + -
19U GLU* 3.0 27.5 + - - +
20U LEU* 2.9 7.4 + - - +
22U ASP* 1.3 74.1 - - + +
24U LYS* 1.3 66.1 + - - +
26U GLU* 3.0 11.7 + - - +
27U LEU* 2.9 23.4 + - - +
49U LEU* 3.4 26.3 - - + +
52U ALA* 3.7 26.9 - - + -
53U ILE* 3.6 21.5 - - + +
56U ILE* 3.4 33.2 - - + -
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Residues in contact with LYS 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680 U 5.2 4.2 + - - -
1R SER 5.9 1.0 + - - -
3R ASP* 4.0 27.1 + - - +
44R GLN* 6.2 0.2 - - - -
20U LEU* 3.0 37.9 + - - +
21U ASP* 4.0 20.9 + - - +
23U LEU* 1.3 75.6 - - - +
25U THR* 1.3 58.3 + - - +
27U LEU* 3.2 6.8 - - + +
28U LEU* 2.8 29.7 + - - +
53U ILE* 4.0 20.4 - - + -
57U LYS* 4.3 23.6 - - - +
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Residues in contact with THR 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLN* 4.6 16.1 + - - +
21U ASP 3.0 14.5 + - - -
22U ASP* 3.3 12.3 + - - -
23U LEU 3.1 0.6 - - - -
24U LYS* 1.3 75.6 - - - +
26U GLU* 1.3 65.9 + - - +
28U LEU* 3.3 7.1 + - + +
29U ASN* 2.9 46.6 + - - +
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Residues in contact with GLU 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U ASP 3.1 11.6 + - - +
23U LEU* 3.0 15.0 + - - +
25U THR* 1.3 77.0 - - - +
27U LEU* 1.3 58.7 + - - +
29U ASN* 3.2 8.9 + - - +
30U ALA* 2.9 28.7 + - + +
45U ARG* 4.0 28.3 + - - +
49U LEU* 3.7 31.8 - - + +
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Residues in contact with LEU 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U LEU 2.9 12.7 + - - +
24U LYS* 3.2 11.9 - - + +
26U GLU* 1.3 77.7 - - - +
28U LEU* 1.3 62.6 - - - +
30U ALA* 2.9 14.3 + - - +
31U ARG* 2.9 49.6 + - - +
46U ILE* 3.8 35.0 - - + +
49U LEU* 3.5 18.3 - - + +
50U ARG* 4.4 13.2 - - + -
53U ILE* 3.8 24.5 - - + -
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Residues in contact with LEU 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ILE* 4.2 21.1 - - + +
6R LYS 3.6 30.3 - - - +
7R HIS* 4.5 2.9 - - - +
8R PRO* 5.0 2.7 - - + +
44R GLN* 3.3 32.5 - - + +
45R TYR* 4.0 20.2 - - + +
24U LYS 2.8 19.9 + - - +
25U THR* 3.7 7.6 - - + +
27U LEU* 1.3 73.6 - - - +
29U ASN* 1.3 62.6 + - - +
31U ARG* 3.4 10.8 + - - +
32U ALA* 3.1 25.7 + - + +
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Residues in contact with ASN 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R TYR* 6.0 0.3 - - - -
80R ARG 5.7 0.7 - - - -
81R ILE* 3.1 31.1 - - + +
25U THR* 2.9 43.4 + - - +
26U GLU* 3.7 7.7 - - - +
28U LEU* 1.3 80.4 - - - +
30U ALA* 1.3 60.4 + - - +
32U ALA* 3.6 6.5 - - - +
33U VAL* 3.1 35.0 + - + +
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Residues in contact with ALA 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U GLU* 2.9 13.6 + - + +
27U LEU* 2.9 13.1 + - - +
29U ASN* 1.3 76.2 - - - +
31U ARG* 1.3 59.5 + - - +
33U VAL* 3.3 8.1 + - - +
34U GLN* 2.9 28.3 + - - +
41U GLU* 6.1 0.2 - - - +
46U ILE* 4.4 25.6 - - + +
49U LEU* 4.6 5.8 - - + -
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Residues in contact with ARG 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560 G 5.7 2.4 + - - -
3R ASP* 5.8 2.2 + - - -
5R ILE 5.6 1.0 + - - -
6R LYS* 3.8 23.2 + - - +
7R HIS* 4.1 18.6 - - + +
27U LEU* 2.9 50.3 + - + +
28U LEU* 3.7 12.7 - - - +
30U ALA* 1.3 74.0 - - - +
32U ALA* 1.3 56.9 + - - +
34U GLN* 3.5 13.2 - - - +
35U ALA* 2.7 34.7 + - - +
46U ILE* 4.4 14.8 - - + +
50U ARG* 4.8 15.0 - - - +
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Residues in contact with ALA 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R PRO* 3.5 37.1 - - + +
10R VAL* 5.0 0.7 - - - +
81R ILE* 4.1 25.1 - - + -
28U LEU 3.1 15.1 + - - +
29U ASN* 3.6 8.1 - - - +
31U ARG* 1.3 74.6 - - - +
33U VAL* 1.3 66.1 + - - +
35U ALA* 3.2 3.4 + - - +
36U ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R ILE 4.6 17.0 - - - -
29U ASN* 3.1 19.3 + - + +
30U ALA* 3.3 8.5 + - - +
32U ALA* 1.3 74.8 - - - +
34U GLN* 1.3 54.6 + - - +
36U ALA* 3.4 8.1 + - - +
38U GLY* 2.7 50.8 + - - +
40U PRO* 4.0 21.1 - - + -
41U GLU* 4.9 7.6 - - + +
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Residues in contact with GLN 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570 C 3.0 48.3 + - - -
580 C 4.1 10.4 + - - -
30U ALA 2.9 16.7 + - - +
31U ARG* 3.5 11.5 - - - +
32U ALA 3.1 0.2 - - - -
33U VAL* 1.3 75.7 - - - +
35U ALA* 1.3 57.8 + - - +
36U ALA 3.0 4.9 - - - -
37U GLY* 2.9 21.1 + - - -
38U GLY 4.5 1.6 - - - +
41U GLU* 3.9 21.7 + - + +
46U ILE* 4.0 18.8 - - - +
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Residues in contact with ALA 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R HIS* 3.8 16.8 - - + +
8R PRO* 3.4 25.6 - - + +
10R VAL* 2.8 20.6 - - + +
31U ARG 2.7 21.1 + - - +
32U ALA* 3.2 7.8 + - - +
34U GLN* 1.3 72.2 - - - +
36U ALA* 1.3 56.8 + - - +
37U GLY 3.2 2.8 + - - -
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Residues in contact with ALA 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R VAL* 3.4 22.8 - - + +
81R ILE 6.5 1.1 - - - -
32U ALA 3.0 14.4 + - - +
33U VAL* 3.8 7.0 - - - +
34U GLN 3.0 1.4 - - - -
35U ALA* 1.3 76.4 - - - +
37U GLY* 1.3 60.7 + - - +
38U GLY* 2.9 7.5 + - - +
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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