Contacts of the helix formed by residues 775 - 782 (chain J) in PDB entry 4E45
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 CYS 775 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 5.9 0.7 - - - -
44F LYS* 4.0 25.5 - - + +
45F GLN* 4.0 11.8 - - - +
48F ALA* 3.9 15.7 - - - -
768J MET* 4.5 2.2 - - - -
771J GLU* 3.5 12.6 - - - -
773J GLY 4.0 0.2 + - - -
774J GLU* 1.3 73.7 - - - +
776J SER* 1.3 69.3 + - - +
777J TYR* 3.7 23.6 - - - -
778J GLU* 3.1 27.4 + - + +
779J LEU* 3.0 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 776 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768J MET* 4.3 9.2 - - - +
771J GLU* 2.4 32.4 + - - -
774J GLU 3.5 3.7 + - - -
775J CYS* 1.3 71.2 - - - +
777J TYR* 1.3 58.1 + - - +
779J LEU* 3.0 12.0 - - - +
780J GLU* 2.9 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 777 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LYS* 3.9 19.6 + - - +
24F HIS* 3.9 28.7 - + + -
48F ALA* 3.6 42.0 - - + -
51F SER* 4.3 4.7 - - - -
52F GLU* 2.7 38.6 + - - -
55F PHE* 5.5 0.5 - - - +
764J MET* 3.4 24.2 - - + -
768J MET* 4.6 2.9 - - - -
775J CYS* 3.2 4.3 - - - -
776J SER* 1.3 79.2 + - - +
778J GLU* 1.3 65.6 + - - +
780J GLU* 3.1 23.4 + - - +
781J VAL* 3.1 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 778 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 3.9 32.4 + - + -
44F LYS* 3.7 31.4 - - - +
775J CYS* 3.1 22.4 + - + +
777J TYR* 1.3 78.2 - - - +
779J LEU* 1.3 64.7 + - - +
780J GLU 3.2 0.2 + - - -
781J VAL* 4.5 1.8 - - - -
782J GLU* 3.0 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 779 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774J GLU* 6.1 3.1 - - + -
775J CYS 3.0 12.6 + - - +
776J SER* 3.0 17.9 - - - +
778J GLU* 1.3 79.3 - - - +
780J GLU* 1.3 57.3 + - + +
782J GLU* 4.4 3.6 + - - +
783J SER* 5.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 780 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLN* 3.3 23.0 + - - +
776J SER* 2.9 18.4 + - - +
777J TYR* 3.1 29.4 + - + +
779J LEU* 1.3 76.0 - - + +
781J VAL* 1.3 64.9 + - + +
783J SER* 5.3 0.7 - - - -
784J TYR* 3.7 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 781 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLN* 3.9 16.2 - - - +
20F LYS* 4.1 14.4 - - + -
21F ALA* 3.2 34.1 - - - +
24F HIS* 4.0 25.6 - - + +
777J TYR* 3.1 40.6 + - + +
778J GLU* 4.1 2.7 - - - +
780J GLU* 1.3 85.2 - - + +
782J GLU* 1.3 61.6 + - - +
783J SER 3.2 3.1 - - - -
784J TYR* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 782 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ALA* 4.9 2.5 - - - -
24F HIS* 6.0 1.1 - - - +
778J GLU* 3.0 31.2 + - + +
779J LEU* 4.4 2.4 + - - +
781J VAL* 1.3 81.3 - - + +
783J SER* 1.3 63.0 + - - +
784J TYR 3.1 1.4 + - - -
785J LEU* 3.1 23.9 + - + +
----------------------------------------------------------
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