Contacts of the helix formed by residues 36 - 44 (chain E) in PDB entry 5IYB
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 36 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E TRP* 3.2 15.9 - - + -
34E ASP* 3.6 11.4 - - - +
35E GLN* 1.3 69.5 - - - +
37E LEU* 1.3 54.4 + - - +
38E GLU* 3.9 7.2 + - - +
39E GLU* 2.6 39.7 + - - +
40E PHE* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E GLU 5.8 0.9 - - - +
7E THR* 4.0 16.4 - - + +
8E TYR* 3.7 40.4 - - + +
11E TRP* 3.2 51.8 - - + +
36E THR* 1.3 74.7 - - - +
38E GLU* 1.3 73.1 + - + +
40E PHE* 3.5 1.4 + - + +
41E LYS* 2.9 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E THR* 3.3 6.0 + - - +
37E LEU* 1.3 91.2 - - + +
39E GLU* 1.3 66.4 + - + +
41E LYS* 3.5 21.0 + - - +
42E ALA* 3.6 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ASP* 5.3 4.2 - - - +
34E ASP* 3.9 4.1 - - - +
35E GLN* 3.9 11.4 - - + -
36E THR* 2.6 47.3 + - - +
38E GLU* 1.3 74.9 - - + +
40E PHE* 1.3 54.2 + - - +
42E ALA* 3.1 6.7 + - - +
43E GLN* 2.6 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E THR* 3.9 17.0 - - + -
10E LEU* 4.9 2.5 - - + -
11E TRP* 3.5 44.2 - + + -
14E ARG* 4.9 12.1 - - + -
35E GLN* 3.3 28.2 + - - +
36E THR 2.8 22.0 + - - +
37E LEU* 3.6 4.5 - - + +
39E GLU* 1.3 72.0 - - - +
41E LYS* 1.3 61.2 + - - +
43E GLN 4.1 0.2 - - - +
44E SER* 2.8 54.8 + - - -
46E ASP* 2.4 33.7 - - - -
58E LEU* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E GLU* 4.5 23.6 + - - +
7E THR* 4.0 21.5 + - + -
37E LEU* 2.9 19.7 + - + +
38E GLU* 3.5 16.2 - - - +
39E GLU 3.2 0.4 - - - -
40E PHE* 1.3 79.6 - - + +
42E ALA* 1.3 56.9 + - - +
45E GLY* 3.4 4.4 - - - -
46E ASP* 3.4 36.3 + - + +
47E LYS 3.3 27.4 + - - +
48E PRO* 4.6 5.9 - - - +
49E SER* 5.0 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLU 3.6 6.0 + - - +
39E GLU* 3.1 6.8 + - - +
40E PHE 3.1 0.2 - - - -
41E LYS* 1.3 79.6 - - - +
43E GLN* 1.3 62.2 + - - +
44E SER 3.3 2.6 - - - -
45E GLY* 3.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLU* 6.1 0.4 - - - +
35E GLN* 3.5 25.4 - - + +
39E GLU* 2.6 23.7 + - + +
40E PHE 3.0 0.2 + - - -
42E ALA* 1.3 73.5 - - - +
44E SER* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E GLN* 5.5 0.2 - - - -
40E PHE* 2.8 51.0 + - - -
42E ALA 4.0 0.9 - - - -
43E GLN* 1.3 77.5 - - - +
45E GLY* 1.3 66.8 + - - +
46E ASP* 3.4 9.1 + - - -
47E LYS* 5.4 0.7 + - - -
57E ASP* 5.7 1.2 - - - +
58E LEU* 4.7 9.2 - - - -
----------------------------------------------------------
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