Contacts of the helix formed by residues 11 - 17 (chain J) in PDB entry 4EMG
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 11 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ASP* 4.6 12.6 - - - +
42I HIS* 6.2 2.5 - - + -
44I ASN* 4.9 5.6 - - - +
79I PHE* 3.7 24.0 - - + -
9J GLU 3.3 3.3 - - - +
10J PRO* 1.3 74.2 - - + +
12J ASP* 1.3 66.3 + - - +
13J LEU 3.0 3.4 - - - -
14J VAL* 3.0 21.5 + - + +
15J ARG* 3.0 13.6 + - + +
39J TYR* 4.7 12.4 + - + +
40J ASP 6.0 1.1 - - - +
41J GLU* 5.3 11.2 - - - +
43J LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ARG* 2.5 45.4 + - - -
9J GLU* 2.8 44.9 + - - +
11J LEU* 1.3 78.3 - - - +
13J LEU* 1.3 54.9 + - - +
15J ARG* 3.1 14.5 + - - +
16J LEU* 2.7 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I VAL* 3.8 16.6 - - + +
77I MSE 4.3 19.1 - - + -
78I LEU 3.9 7.0 - - - +
79I PHE* 3.5 39.0 - - + +
9J GLU 4.2 0.4 + - - -
10J PRO 3.3 13.0 + - - +
11J LEU 3.0 0.4 - - - -
12J ASP* 1.3 80.5 - - - +
14J VAL* 1.3 60.4 + - + +
16J LEU* 3.7 9.8 + - + +
17J SER* 2.9 27.8 + - - +
88J ILE* 4.1 2.5 - - + +
90J PRO* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 4.2 15.0 - - + -
11J LEU* 3.0 26.1 + - + +
13J LEU* 1.3 76.9 - - + +
15J ARG* 1.3 59.1 + - - +
17J SER* 3.0 24.8 + - - -
18J LEU 3.6 0.3 + - - -
36J LEU* 3.3 20.6 - - + +
39J TYR* 3.8 36.6 - - + -
43J LEU* 4.4 4.0 - - + -
45J MSE 5.2 2.7 - - - -
88J ILE* 3.8 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLU* 4.3 16.4 + - - +
12F ASP* 2.6 43.0 + - - -
15F ARG* 4.4 15.0 - - - +
11J LEU 3.0 11.2 + - - +
12J ASP* 3.5 16.1 + - - +
14J VAL* 1.3 78.6 - - - +
16J LEU* 1.3 64.8 + - + +
17J SER 3.3 0.9 + - - -
18J LEU* 3.3 26.6 + - + +
39J TYR* 3.1 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ASP* 2.7 36.0 + - + +
13J LEU* 4.2 9.2 - - + +
15J ARG* 1.3 76.8 - - + +
17J SER* 1.3 60.0 + - - +
18J LEU 3.3 3.3 + - - +
20J GLU* 4.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LEU* 2.9 17.2 + - - +
14J VAL* 3.0 16.3 + - - -
16J LEU* 1.3 76.0 - - - +
18J LEU* 1.3 66.8 + - - +
19J ASP 3.1 0.9 + - - -
20J GLU* 2.8 25.8 + - - +
22J VAL* 3.6 21.4 - - - +
36J LEU* 3.7 11.3 - - - +
88J ILE* 5.6 2.1 - - - +
90J PRO* 3.3 28.5 - - - +
----------------------------------------------------------
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