Contacts of the helix formed by residues 36 - 49 (chain F) in PDB entry 5ZX2
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 LEU 36 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ASP 3.3 21.1 - - - +
33F ALA 2.9 11.0 + - - +
34F ILE 2.9 0.4 + - - -
35F PRO* 1.3 83.4 - - + +
37F LEU* 1.3 63.7 + - - +
38F ASP 3.4 0.7 - - - -
39F GLN* 2.9 16.1 + - + +
40F LEU* 2.8 33.6 + - + +
78F LEU* 4.2 9.9 - - + -
79F LYS* 3.7 41.1 - - + +
82F LEU* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D ILE* 4.5 10.8 - - + -
366D ILE* 3.8 22.0 - - + -
369D ASN* 4.3 14.8 - - - +
33F ALA 4.9 2.7 - - - +
34F ILE* 2.9 32.3 + - + +
35F PRO 3.3 0.4 - - - -
36F LEU* 1.3 73.9 - - - +
38F ASP* 1.3 62.3 + - - +
39F GLN 2.9 0.9 + - - -
40F LEU* 2.9 5.6 + - + +
41F TYR* 2.8 34.0 + - - +
58F LEU* 4.3 18.5 - - + +
62F MET* 3.6 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLY 4.1 5.5 - - - +
285C GLU* 3.4 48.5 - - + +
286C PRO* 4.3 6.8 - - + +
34F ILE 4.8 0.2 + - - -
35F PRO 4.4 6.5 + - - +
36F LEU 3.4 0.6 - - - -
37F LEU* 1.3 79.7 - - - +
39F GLN* 1.3 60.9 + - + +
41F TYR* 4.3 8.1 - - - +
42F GLY 3.8 4.7 + - - -
31G G 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F PRO 4.9 3.6 + - - +
36F LEU* 2.9 22.1 + - + +
37F LEU 2.9 0.4 + - - -
38F ASP* 1.3 76.9 - - + +
40F LEU* 1.3 67.8 + - + +
42F GLY* 2.9 15.2 + - - -
43F GLY 3.2 7.4 + - - -
79F LYS* 2.4 44.0 + - - +
83F TYR* 4.4 8.1 + - + +
31G G 4.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 2.8 32.2 + - + +
37F LEU* 2.9 4.2 + - + +
39F GLN* 1.3 72.4 - - + +
41F TYR* 1.3 62.6 + - - +
43F GLY* 2.9 5.0 + - - +
44F ALA* 2.9 21.1 + - - +
58F LEU* 3.6 17.3 - - + -
61F THR* 5.6 0.9 - - + -
62F MET* 3.8 19.1 - - + -
79F LYS* 4.6 3.8 - - + +
82F LEU* 3.7 35.7 - - + +
83F TYR* 3.5 52.7 - - + +
86F LEU* 3.9 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU 2.8 21.5 + - - +
38F ASP* 4.4 9.0 - - - +
40F LEU* 1.3 72.8 - - - +
42F GLY* 1.3 66.8 + - - +
44F ALA* 2.9 16.0 + - - +
45F LEU* 3.0 34.5 + - + +
51F PRO* 3.7 26.9 + - - +
54F ALA* 3.6 30.5 - - + -
55F GLU* 3.9 24.7 + - + +
58F LEU* 3.7 22.5 - - + +
31G G 5.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASP 3.8 3.2 + - - -
39F GLN 2.9 8.7 + - - -
41F TYR* 1.3 83.5 - - - +
43F GLY* 1.3 61.4 + - - +
45F LEU* 3.7 18.6 - - - +
46F ARG* 3.7 7.4 - - - +
31G G 3.0 47.9 - - - +
32G G 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN 3.2 6.1 + - - -
40F LEU 2.9 8.8 + - - -
42F GLY* 1.3 75.2 - - - +
44F ALA* 1.3 64.8 + - - +
46F ARG* 2.9 30.7 + - - +
47F MET* 3.5 10.4 + - - +
83F TYR* 3.8 25.5 + - - -
86F LEU* 4.2 5.6 - - - -
31G G 3.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU 2.9 11.5 + - - +
41F TYR* 2.9 11.2 + - - +
43F GLY* 1.3 75.6 - - - +
45F LEU* 1.3 63.7 + - - +
47F MET* 3.0 5.7 + - - +
48F THR* 2.9 24.9 + - - +
54F ALA* 3.7 25.4 - - + +
57F LEU* 3.7 22.2 - - + -
58F LEU* 4.6 1.1 - - + +
86F LEU* 3.8 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 3.0 32.9 + - + +
42F GLY* 3.7 14.8 - - - +
44F ALA* 1.3 75.4 - - - +
46F ARG* 1.3 59.6 + - - +
47F MET 2.9 0.5 + - - -
48F THR* 3.8 3.4 - - - -
49F ARG* 2.4 35.0 + - - +
50F ASN 3.9 30.3 - - - +
51F PRO* 4.1 6.7 - - + -
54F ALA* 3.8 10.0 - - + +
32G G 3.7 60.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ARG* 4.2 24.7 - - - +
402C GLU* 5.2 4.6 + - - -
42F GLY 3.7 8.7 - - - +
43F GLY* 2.9 12.5 + - - +
45F LEU* 1.3 79.0 - - - +
47F MET* 1.3 63.2 + - + +
49F ARG* 3.7 19.2 + - - +
83F TYR* 4.6 6.3 + - - -
30G G 3.1 49.1 + - - +
31G G 3.6 24.8 + - - -
32G G 3.9 32.2 + - - +
33G A 5.4 0.9 + - - -
23H A 4.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLY* 3.7 13.2 - - - +
44F ALA 3.0 5.5 + - - +
46F ARG* 1.3 80.4 - - + +
48F THR* 1.3 62.8 + - + +
49F ARG* 4.0 5.9 + - - -
57F LEU* 4.4 7.4 - - + -
83F TYR* 5.2 7.0 - - + -
86F LEU* 3.7 23.3 - - + -
87F THR* 3.5 34.5 - - + -
90F TYR* 3.2 51.2 + - + -
91F ILE* 6.1 0.4 - - - -
30G G 6.2 0.2 - - - +
23H A 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ALA 2.9 16.1 + - - +
45F LEU* 3.6 0.9 + - - -
47F MET* 1.3 77.6 - - - +
49F ARG* 1.3 73.8 + - - +
50F ASN* 2.8 29.2 + - - +
53F ASP* 3.7 41.2 - - + +
54F ALA* 3.4 7.6 + - - +
57F LEU* 4.1 15.5 - - + -
90F TYR* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ARG* 4.0 18.5 - - - +
396D ASN* 5.7 1.0 - - - +
45F LEU* 2.4 32.0 + - - +
46F ARG 3.7 17.7 + - - +
47F MET 4.1 6.0 + - - -
48F THR* 1.3 67.6 + - - +
50F ASN* 1.3 56.1 + - - +
51F PRO* 4.8 0.4 - - - -
90F TYR* 5.3 1.2 + - - -
32G G 4.2 31.8 + - - +
33G A 3.9 33.9 + - - +
22H T 2.4 43.3 + - - +
23H A 3.6 15.0 - - - +
----------------------------------------------------------
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