Contacts of the helix formed by residues 33 - 42 (chain F) in PDB entry 4P9U
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 ALA 33 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F PRO* 1.3 77.5 - - - +
34F GLU* 1.3 66.4 + - - +
35F ARG* 3.2 3.6 - - + +
36F GLU* 2.9 36.1 + - - +
37F LEU* 3.1 10.0 + - - +
11G T 3.7 33.5 + - - +
12G G 3.3 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F PRO 3.6 2.1 + - - +
33F ALA* 1.3 69.9 - - - +
35F ARG* 1.3 58.4 + - + +
37F LEU* 3.4 2.3 + - - +
38F SER* 2.9 29.6 + - - -
45F ARG* 2.7 47.5 + - + +
48F LEU* 4.0 17.1 - - + +
49F ARG* 2.9 29.2 + - - +
52F LEU* 3.7 27.1 - - + +
63F ILE* 5.1 2.1 - - - +
69F THR* 4.8 1.4 + - - +
12G G 3.0 45.3 + - - +
13G G 3.7 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ALA* 3.2 3.2 - - + +
34F GLU* 1.3 77.9 - - - +
36F GLU* 1.3 69.3 + - - +
38F SER* 2.8 23.7 + - - -
39F GLU* 3.7 14.0 + - - +
45F ARG* 4.0 24.0 - - - +
11G T 4.1 24.9 + - - +
12G G 3.0 53.1 + - - -
13G G 3.8 4.8 + - - -
18H A 5.1 0.8 - - - +
19H C 3.3 23.2 - - - +
20H C 4.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F PRO* 4.4 9.4 - - + -
33F ALA* 2.9 35.0 + - - +
35F ARG* 1.3 86.5 - - - +
37F LEU* 1.3 60.0 + - - +
38F SER 3.2 0.2 - - - -
39F GLU* 3.1 20.4 - - + +
40F LEU* 2.9 28.7 + - - +
11G T 4.3 14.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
15F TYR* 4.7 0.7 - - + -
16F ILE* 4.8 12.1 - - + -
25F PHE* 4.1 15.5 - - + -
31F LEU* 3.9 37.2 - - + -
32F PRO* 4.1 20.2 - - + +
33F ALA 3.1 9.7 + - - +
34F GLU* 4.1 3.6 - - - +
36F GLU* 1.3 73.6 - - - +
38F SER* 1.3 65.4 + - - +
39F GLU 3.1 0.7 - - - -
40F LEU* 3.5 28.0 - - + -
41F ILE* 2.9 50.3 + - + +
43F VAL* 4.8 0.2 - - - +
48F LEU* 4.2 19.1 - - + -
52F LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F GLU 2.9 16.9 + - - -
35F ARG* 2.8 20.1 + - - -
37F LEU* 1.3 76.8 - - - +
39F GLU* 1.3 58.8 + - - +
42F GLY* 3.5 14.7 + - - -
43F VAL* 2.8 33.3 + - - +
44F THR* 4.3 0.7 - - - -
45F ARG* 4.0 25.4 - - - +
48F LEU* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 4.0 32.9 + - + +
35F ARG 3.7 13.2 - - - +
36F GLU* 3.1 25.4 - - - +
38F SER* 1.3 80.3 + - - +
40F LEU* 1.3 63.0 + - + +
41F ILE 3.5 0.4 - - - -
42F GLY* 4.5 4.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
6B LYS* 5.9 6.5 - - + -
11B PHE* 3.1 46.5 - - + -
15F TYR* 4.3 8.4 + - - +
24F ARG* 3.8 33.4 - - - +
25F PHE* 4.4 9.2 - - + -
32F PRO* 5.4 5.2 - - + -
36F GLU 2.9 17.0 + - - +
37F LEU* 3.2 26.6 + - + -
39F GLU* 1.3 80.7 - - + +
41F ILE* 1.3 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.9 20.1 - - - -
41B ILE 5.1 1.2 - - - +
11F PHE* 4.1 24.8 - - + -
12F ALA* 4.2 14.1 - - - +
15F TYR* 3.6 36.6 - - + -
16F ILE* 4.1 16.8 - - + -
37F LEU* 2.9 32.1 + - + +
40F LEU* 1.3 81.5 - - - +
42F GLY* 1.3 59.0 + - - +
43F VAL* 3.7 24.7 - - + -
48F LEU* 4.2 15.7 - - + -
----------------------------------------------------------
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 SER 3.5 10.6 + - - -
39F GLU* 4.5 3.7 - - - -
40F LEU 3.8 0.8 - - - -
41F ILE* 1.3 80.2 - - - +
43F VAL* 1.3 65.9 + - - +
15H T 4.6 6.1 + - - -
----------------------------------------------------------
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