Contacts of the helix formed by residues 37 - 51 (chain J) in PDB entry 2ZP8
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 37 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C THR 4.6 0.2 - - - -
34D HIS* 3.3 4.0 - - - -
35D SER 3.3 20.2 - - - +
36D GLU* 4.0 7.9 - - - +
37D LYS* 3.5 30.7 - - + +
6J ASP 4.6 2.7 - - - +
7J ASP* 2.4 33.8 + - - +
8J LEU* 2.7 17.9 + - - +
9J GLU* 4.7 0.2 - - - +
10J VAL* 4.7 5.6 - - + -
35J ILE 4.1 0.6 + - - -
36J LEU* 1.3 75.3 - - - +
38J ALA* 1.3 66.2 + - - +
39J GLN* 3.9 4.0 - - - -
40J GLY 2.9 11.1 + - - -
41J TYR* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 4.1 9.0 - - + -
30C THR 3.2 20.4 - - - +
31C ARG* 3.6 7.3 - - - -
32C PHE* 3.3 22.7 - - + -
34D HIS* 2.9 9.4 - - + -
36D GLU* 3.1 18.9 + - - +
1H MET* 3.8 8.3 - - + -
37J THR* 1.3 74.2 - - - +
39J GLN* 1.3 52.8 + - - +
41J TYR 3.3 0.9 + - - -
42J THR* 2.5 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 3.0 30.9 - - + -
36D GLU* 4.7 1.4 + - - +
1H MET* 3.3 18.6 - - + +
2H VAL* 3.7 1.7 + - - +
3H ILE* 2.9 40.9 + - - +
3J ILE* 3.6 27.3 - - + +
7J ASP* 3.5 18.2 - - + +
8J LEU* 4.0 12.1 - - + -
37J THR* 3.1 1.9 - - - +
38J ALA* 1.3 77.5 - - - +
40J GLY* 1.3 61.9 + - - +
42J THR* 3.4 3.3 - - - -
43J LEU* 3.3 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I PHE* 3.4 33.1 - - - -
8J LEU* 3.9 17.0 - - - +
36J LEU* 4.6 2.7 - - - -
37J THR* 2.9 14.4 + - - -
39J GLN* 1.3 75.1 - - - +
41J TYR* 1.3 63.5 + - - -
43J LEU 3.3 2.4 + - - -
44J LEU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA 5.7 0.4 - - - -
29C ASP* 3.5 37.0 + - - +
30C THR* 3.4 36.6 - - - +
31C ARG* 4.0 8.1 - - + -
33D HIS 4.1 21.4 + - - -
34D HIS* 4.6 7.9 - - + -
36J LEU* 3.7 31.9 - - + +
37J THR 3.1 12.2 + - - -
38J ALA 3.8 0.2 - - - +
40J GLY* 1.3 70.0 - - - +
42J THR* 1.3 61.4 + - - +
43J LEU 3.0 0.5 + - - -
44J LEU* 3.0 13.9 + - + -
45J ASP* 2.7 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 3.4 16.6 - - - +
32C PHE* 3.3 18.3 + - - +
3H ILE 4.1 8.1 - - - +
4H ALA* 3.9 6.1 - - - -
5H THR* 3.4 44.3 + - - +
8H LEU* 4.1 6.9 - - + +
38J ALA 2.5 23.4 + - - -
39J GLN* 3.4 13.9 - - - +
41J TYR* 1.3 76.5 - - - +
43J LEU* 1.3 56.9 + - + +
45J ASP* 4.4 1.7 - - - +
46J PHE* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 3.7 31.0 - - + -
8H LEU* 4.2 5.6 - - + -
43H LEU* 4.2 13.0 - - + -
43I LEU* 3.8 29.6 - - + -
46I PHE* 4.6 3.1 - - + -
47I ILE* 4.4 11.0 - - + -
3J ILE* 5.0 9.0 - - + -
8J LEU* 4.0 22.4 - - + -
39J GLN* 3.5 24.0 - - - +
40J GLY 3.3 5.0 + - - +
41J TYR 3.1 0.8 - - - -
42J THR* 1.3 76.3 - - - +
44J LEU* 1.3 57.0 + - - +
46J PHE* 3.0 5.3 + - - +
47J ILE* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I PHE* 4.5 7.2 - - + -
47I ILE* 4.4 23.5 - - + +
50I HIS* 3.5 50.0 - - + +
51I LEU* 3.7 11.4 - - + +
36J LEU* 4.4 13.7 - - + -
40J GLY 3.0 18.1 + - - +
41J TYR* 3.9 13.9 - - + +
43J LEU* 1.3 75.7 - - - +
45J ASP* 1.3 58.6 + - - +
47J ILE* 3.9 1.6 - - - +
48J GLN* 2.8 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP* 3.6 20.8 - - - +
31C ARG* 4.6 22.7 + - + +
41J TYR* 2.7 25.4 + - + +
42J THR* 4.4 2.2 - - - +
44J LEU* 1.3 73.9 - - - +
46J PHE* 1.3 62.0 + - - +
48J GLN* 4.0 5.1 - - - +
49J LYS* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H THR* 5.5 4.0 - - + +
8H LEU* 3.4 42.6 - - + -
9H GLU* 3.7 20.6 - - + -
36H LEU* 4.3 9.0 - - + -
40H GLY* 3.5 42.4 - - - -
43H LEU* 5.1 2.5 - - + -
44H LEU* 4.6 7.0 - - + -
42J THR 3.2 19.8 + - - +
43J LEU* 3.0 5.0 + - - +
45J ASP* 1.3 80.2 - - - +
47J ILE* 1.3 82.7 + - + +
49J LYS* 3.3 2.9 + - - +
50J HIS* 3.2 52.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 4.1 26.2 - - + -
44H LEU* 4.3 15.0 - - + +
47H ILE* 4.0 29.8 - - + -
43I LEU* 6.0 0.7 - - + -
47I ILE* 3.9 25.4 - - + -
51I LEU* 3.9 21.1 - - + -
43J LEU* 2.7 24.8 + - + +
44J LEU* 3.9 3.1 - - - +
46J PHE* 1.3 87.6 - - + +
48J GLN* 1.3 65.1 + - - +
49J LYS 3.0 0.7 + - - -
50J HIS 3.0 1.4 + - - -
51J LEU* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 3.5 22.6 - - + +
52I ASN* 3.2 50.3 + - - +
53I LYS 4.7 1.8 + - - +
44J LEU* 2.8 33.4 + - + +
45J ASP* 4.0 5.2 - - - +
47J ILE* 1.3 74.8 - - - +
49J LYS* 1.3 63.4 + - - +
51J LEU* 4.2 9.4 + - - +
53J LYS* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H GLU* 4.2 23.9 + - - +
17H ARG* 5.9 1.0 - - - +
32H LYS* 4.2 15.9 + - - +
34H VAL* 5.1 7.5 - - - +
45J ASP* 3.0 25.3 + - - +
46J PHE* 3.6 5.4 - - - +
47J ILE 3.1 0.2 - - - -
48J GLN* 1.3 80.1 - - - +
50J HIS* 1.3 72.0 + - + +
53J LYS* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H GLU* 2.7 35.9 + - - -
32H LYS* 3.9 29.3 - - + +
34H VAL* 5.2 2.9 - - + -
36H LEU* 3.5 23.5 - - + +
44H LEU* 3.7 33.5 - - + +
46J PHE* 3.2 42.7 + + - -
47J ILE 3.0 2.6 + - - -
49J LYS* 1.3 93.0 - - + +
51J LEU* 1.3 64.8 + - - +
52J ASN 3.5 1.7 + - - -
53J LYS* 3.5 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 3.8 25.9 - - + +
47H ILE* 3.9 15.5 - - + -
48H GLN* 3.7 35.9 - - + +
51H LEU* 3.8 28.9 - - + -
51I LEU* 4.1 9.4 - - + -
47J ILE* 2.9 24.6 + - + +
48J GLN* 4.2 7.0 + - - +
49J LYS 3.5 1.5 - - - +
50J HIS* 1.3 77.9 - - - +
52J ASN* 1.3 83.8 + - - +
53J LYS* 3.6 13.9 + - - +
----------------------------------------------------------
Back to top of page
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