Contacts of the helix formed by residues 21 - 29 (chain L) in PDB entry 2EHO
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 SER 21 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L VAL* 3.8 13.3 + - - +
9L GLU 3.7 17.3 - - - -
10L SER* 3.3 16.5 + - - -
18L ASN* 3.0 9.7 + - - -
19L PHE 3.5 0.2 - - - -
20L LEU* 1.3 72.8 - - - +
22L LEU* 1.3 65.9 + - - +
23L ASP* 3.3 7.3 + - - +
24L ASP* 3.0 36.2 + - - +
25L ILE* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ILE* 4.3 16.7 - - + +
13J LEU* 3.7 30.7 - - + -
14J HIS* 3.9 23.3 - - + +
78J ALA* 3.8 25.8 - - + +
79J TYR 5.1 0.4 - - - +
82J ASP* 3.8 24.9 - - + +
86J ARG* 4.6 1.8 - - - +
7L ARG* 4.8 17.7 - - + +
8L VAL* 4.8 6.1 + - - +
20L LEU 3.8 11.9 - - - +
21L SER* 1.3 71.2 - - - +
23L ASP* 1.3 65.0 + - - +
25L ILE* 3.0 10.6 + - - +
26L LEU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J HIS* 3.7 14.2 + - - -
7L ARG* 2.6 43.1 + - - -
8L VAL 4.3 3.8 - - - +
9L GLU* 5.4 0.2 - - - -
10L SER* 4.0 19.5 + - - +
21L SER* 3.0 9.9 + - - +
22L LEU* 1.3 76.9 - - - +
24L ASP* 1.3 57.3 + - - +
26L LEU* 3.5 8.6 + - - +
27L MSE 3.0 28.3 + - - +
115L HIS* 3.9 8.9 - - + -
170L GLU* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J ARG* 3.8 14.4 - - - +
10L SER* 2.4 29.1 + - - -
11L GLY 2.8 16.2 + - - -
12L ALA* 3.6 14.5 + - - +
17L GLU* 3.5 15.0 - - + +
18L ASN 2.7 26.0 + - - -
21L SER* 2.9 21.6 + - - +
23L ASP* 1.3 73.3 - - - +
25L ILE* 1.3 58.0 + - - +
27L MSE 3.3 7.7 + - - +
28L SER* 2.7 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J MSE 3.8 10.8 - - - -
10J ILE* 4.0 17.3 - - + -
71J ARG* 3.1 28.9 + - - +
74J ARG* 3.0 50.5 - - + +
75J CYS* 3.7 22.4 - - - -
78J ALA* 4.6 10.3 - - + -
19L PHE 4.0 5.6 - - - +
21L SER 2.9 21.6 + - - +
22L LEU* 3.3 9.4 - - - +
24L ASP* 1.3 75.7 - - - +
26L LEU* 1.3 66.1 + - - +
28L SER* 3.0 20.3 + - - -
29L HIS* 3.3 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J MSE 3.3 28.6 - - + +
10J ILE* 3.4 16.2 - - + -
11J ARG* 3.9 17.0 - - + +
14J HIS* 3.4 50.3 - - + +
22L LEU 2.9 22.3 + - - +
23L ASP* 3.5 9.0 - - - +
25L ILE* 1.3 77.3 - - - +
27L MSE 1.3 62.8 + - - +
29L HIS* 3.4 13.7 + - - +
30L GLU* 4.0 9.5 + - - +
115L HIS* 4.0 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ALA* 3.5 28.5 - - + -
17L GLU* 3.8 22.4 - - + +
23L ASP 3.0 17.5 + - - +
24L ASP* 3.5 9.4 - - - +
25L ILE 3.1 0.2 - - - -
26L LEU* 1.3 78.4 - - - +
28L SER* 1.3 62.4 + - - +
29L HIS 3.3 3.3 + - - -
30L GLU* 3.4 20.6 - - - +
70L LEU* 3.8 10.5 - - - -
115L HIS* 3.6 31.4 + - + +
118L GLY* 4.1 5.2 - - - -
119L PHE* 3.7 36.1 - - - +
122L GLN* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J ARG* 3.8 4.9 + - - -
74J ARG* 3.8 4.7 + - - -
17L GLU* 3.2 26.1 + - - -
24L ASP 2.7 23.0 + - - -
25L ILE* 3.0 11.8 + - - -
27L MSE 1.3 79.7 - - - +
29L HIS* 1.3 60.6 + - - +
30L GLU 3.2 2.2 - - - -
70L LEU* 3.5 13.1 + - - -
71L TRP* 3.1 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J PHE 4.0 7.1 + - - -
4J GLU* 3.0 37.0 + - - -
7J MSE 3.4 39.0 - - + +
11J ARG* 4.1 12.6 + - - -
71J ARG* 3.8 11.4 - - - +
25L ILE 3.3 1.2 + - - +
26L LEU 3.7 10.5 - - - +
27L MSE 3.2 1.0 - - - -
28L SER* 1.3 78.4 - - - +
30L GLU* 1.3 63.3 + - + +
31L LYS* 2.8 41.5 + - - -
69L PRO* 3.6 9.1 - - + +
71L TRP* 4.1 17.9 - - - -
----------------------------------------------------------
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