Contacts of the helix formed by residues 21 - 28 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.8 14.0 + - - +
9D GLU 3.7 11.4 - - - -
10D SER* 3.8 4.3 - - - -
18D ASN* 2.9 24.2 + - - +
19D PHE 3.4 0.2 - - - -
20D LEU* 1.3 74.5 - - - +
22D LEU* 1.3 61.7 + - - +
23D ASP* 3.3 8.8 + - - +
24D ASP* 2.7 37.6 + - - +
25D ILE* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.2 27.4 - - + +
13B LEU* 4.1 23.6 - - + -
14B HIS* 4.9 6.3 - - + +
78B ALA* 4.0 33.9 - - + +
79B TYR* 4.5 2.9 - - - +
82B ASP* 3.6 35.4 - - + +
86B ARG* 4.7 4.7 - - - +
5D TYR* 5.2 1.1 - - - +
7D ARG* 6.3 0.7 - - - +
8D VAL* 4.5 3.6 + - - +
20D LEU 3.3 4.2 + - - +
21D SER* 1.3 71.7 - - - +
23D ASP* 1.3 65.4 + - - +
25D ILE* 3.2 10.5 - - + +
26D LEU* 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B HIS* 5.7 5.9 + - - -
7D ARG* 2.5 37.6 + - - +
8D VAL 5.4 1.7 + - - +
10D SER* 4.4 17.0 - - - +
21D SER* 3.1 6.4 + - - +
22D LEU* 1.3 81.8 - - - +
24D ASP* 1.3 57.7 + - - +
26D LEU* 3.3 11.9 + - - +
27D MSE 2.9 28.1 + - - +
115D HIS* 4.1 15.5 + - + -
170D GLU* 5.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.6 14.4 - - - +
10D SER* 3.3 7.5 + - - -
11D GLY 3.0 20.1 + - - -
12D ALA* 3.0 31.2 + - - +
17D GLU* 3.4 14.2 - - + +
18D ASN 2.9 23.0 + - - -
21D SER* 2.7 29.3 + - - +
23D ASP* 1.3 72.7 - - - +
25D ILE* 1.3 64.8 + - - +
27D MSE 3.6 6.0 - - - +
28D SER* 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MSE 3.3 33.0 - - - -
10B ILE* 3.4 32.8 - - + -
71B ARG* 2.8 28.2 + - - +
74B ARG* 3.4 38.8 - - + +
75B CYS* 4.3 7.9 - - - -
78B ALA* 4.8 8.7 - - + -
19D PHE 4.3 4.9 - - - +
21D SER 3.0 19.0 + - - +
22D LEU* 3.2 13.5 - - + +
24D ASP* 1.3 76.1 - - - +
26D LEU* 1.3 68.2 + - - +
28D SER* 3.0 5.9 + - - -
29D HIS* 3.4 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MSE 3.9 12.2 - - + +
10B ILE* 3.5 36.8 - - + -
11B ARG* 4.3 13.9 - - + +
14B HIS* 3.9 29.6 - - + +
1016B SO4 3.5 25.1 - - - +
22D LEU* 3.0 13.4 + - + +
23D ASP* 3.3 12.3 - - - +
25D ILE* 1.3 83.3 - - - +
27D MSE 1.3 62.7 + - - +
29D HIS* 3.5 12.1 + - - +
30D GLU* 3.8 9.7 - - - +
115D HIS* 4.2 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 3.4 22.7 - - + -
17D GLU* 3.7 21.8 - - + +
23D ASP 2.9 17.4 + - - +
24D ASP* 3.6 9.2 - - - +
25D ILE 3.3 0.2 - - - -
26D LEU* 1.3 72.1 - - - +
28D SER* 1.3 72.7 + - - +
29D HIS 2.8 10.6 + - - -
30D GLU* 3.1 23.7 + - - +
70D LEU* 4.0 4.9 - - - -
115D HIS* 3.5 40.8 + - + -
118D GLY* 4.1 4.5 - - - +
119D PHE* 3.9 32.7 - - + +
122D GLN* 3.3 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ARG* 3.3 10.7 + - - -
74B ARG* 3.4 5.1 + - - -
17D GLU* 3.4 28.3 + - - -
24D ASP 3.0 11.6 + - - -
25D ILE 3.0 13.0 + - - -
27D MSE 1.3 86.4 - - - +
29D HIS* 1.3 55.5 + - - +
30D GLU 3.3 2.9 - - - -
70D LEU* 3.3 13.9 + - - -
71D TRP* 3.1 38.4 + - - -
----------------------------------------------------------
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