Contacts of the strand formed by residues 792 - 799 (chain A) in PDB entry 4D86
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 792 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LYS* 1.3 71.9 - - - +
793A PHE* 1.3 64.0 + - - +
794A SER* 3.7 12.6 - - - -
795A ARG* 3.6 43.5 - - - +
805A ILE* 3.9 8.5 - - - -
806A VAL 3.7 7.6 - - - -
807A GLN* 4.1 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LYS* 3.4 20.6 - - + -
792A CYS* 1.3 75.9 - - - +
794A SER* 1.3 60.6 + - - +
806A VAL* 2.8 20.9 + - + +
808A GLN* 4.3 14.8 - - + -
964A GLU* 3.7 30.5 - - + -
967A VAL* 3.3 32.8 - - + -
968A GLU* 3.6 32.1 - - + -
971A ALA* 4.4 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A CYS* 3.7 3.0 - - - -
793A PHE* 1.3 81.2 - - - +
795A ARG* 1.3 67.2 + - - +
796A THR* 4.6 9.4 + - - -
804A LEU 4.0 1.2 + - - +
805A ILE* 3.5 2.9 - - - -
806A VAL* 2.9 48.8 + - - +
971A ALA* 4.1 14.0 - - - +
974A VAL* 4.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A CYS* 3.6 21.8 - - - +
794A SER* 1.3 80.3 - - - +
796A THR* 1.3 62.0 + - - +
797A VAL* 4.2 1.5 + - - +
803A VAL* 4.1 19.7 - - + +
804A LEU 3.4 5.2 - - - -
805A ILE* 3.4 45.2 - - + +
807A GLN* 5.1 2.4 + - - -
958A TYR* 4.6 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A SER* 4.6 5.2 + - - -
795A ARG* 1.3 76.5 + - - +
797A VAL* 1.3 70.2 + - - +
798A LEU* 3.3 12.3 + - + +
803A VAL* 3.9 2.9 - - - +
804A LEU* 2.8 46.7 + - - +
974A VAL* 3.2 31.7 - - + +
978A PHE* 4.6 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ARG 4.2 1.7 + - - +
796A THR* 1.3 77.0 - - - +
798A LEU* 1.3 63.9 + - - +
799A ALA 3.6 23.3 - - - +
800A PRO* 5.3 1.6 - - + -
801A GLY 5.6 0.9 - - - +
802A VAL 3.5 7.6 - - - +
803A VAL* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A THR* 3.8 19.1 - - + +
797A VAL* 1.3 76.7 - - - +
799A ALA* 1.3 63.6 + - + +
802A VAL* 2.8 24.1 + - + +
804A LEU* 4.0 19.7 - - + +
941A ILE* 4.0 18.4 - - + +
942A LYS* 5.6 0.7 - - - -
945A PHE* 3.9 33.7 - - + -
957A ILE* 4.5 2.0 - - + -
978A PHE* 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A VAL* 3.6 12.2 - - - +
798A LEU* 1.3 81.0 - - + +
800A PRO* 1.4 83.4 - - + +
801A GLY 3.1 0.5 + - - -
802A VAL* 3.0 29.5 + - + +
945A PHE* 5.4 10.8 - - + +
----------------------------------------------------------
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