Contacts of the strand formed by residues 780 - 789 (chain A) in PDB entry 5C58
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 780 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A GLY 3.1 13.5 - - - +
774A ARG* 3.2 9.7 - - - +
775A ALA* 2.8 28.6 + - + +
776A PHE* 3.5 31.9 - - + -
779A LYS* 1.3 72.9 - - - +
781A ASP* 1.3 64.9 + - - +
782A ALA* 3.5 9.0 + - + +
817A ALA* 5.5 4.7 - - + -
818A SER 3.8 9.9 - - - +
819A TYR* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN* 3.8 22.6 + - - +
700A TYR* 3.0 39.4 + - - -
773A GLY 3.5 3.6 - - - +
774A ARG* 3.5 18.9 + - + +
779A LYS* 3.7 9.1 - - + +
780A LEU* 1.3 72.4 - - - +
782A ALA* 1.3 62.2 + - - +
816A TYR* 4.8 3.9 - - - -
817A ALA* 3.1 2.6 - - - +
818A SER* 2.7 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A TYR* 4.6 0.2 - - - -
771A LEU 4.4 0.2 - - - +
772A GLY* 3.3 1.1 - - - -
773A GLY* 2.8 38.8 + - - +
780A LEU* 3.5 11.0 + - + +
781A ASP* 1.3 78.7 + - - +
783A GLY* 1.3 56.4 + - - +
816A TYR* 3.4 18.6 - - - +
817A ALA* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A LEU 3.2 13.9 - - - -
772A GLY* 3.6 6.1 - - - -
782A ALA* 1.3 75.3 - - - +
784A VAL* 1.3 61.0 + - - +
815A LEU* 3.8 5.0 - - - +
816A TYR* 3.2 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A VAL 3.5 3.1 - - - +
770A THR* 3.2 3.0 - - - -
771A LEU* 3.0 50.0 + - + +
783A GLY* 1.3 74.6 - - - -
785A THR* 1.3 65.5 + - - +
786A VAL* 4.3 19.6 - - + +
813A PHE* 4.4 14.1 - - + -
814A ASP 3.3 13.2 - - - +
815A LEU* 3.7 19.5 - - + -
816A TYR* 3.8 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 4.7 10.0 - - - +
145A GLN* 4.3 17.8 + - + +
768A SER* 4.8 4.0 - - - -
769A VAL 3.7 2.5 - - - -
770A THR* 3.2 28.0 - - + +
783A GLY 4.3 0.2 - - - -
784A VAL* 1.3 70.5 - - - +
786A VAL* 1.3 64.9 + - - +
787A ARG* 3.7 25.1 + - + -
814A ASP* 2.8 47.5 + - - +
816A TYR* 3.7 18.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A SER* 3.2 8.3 - - - -
769A VAL* 2.9 52.2 + - + +
771A LEU* 6.5 0.7 - - + -
784A VAL* 4.3 10.8 - - + +
785A THR* 1.3 72.3 - - - +
787A ARG* 1.3 63.3 + - - +
788A PHE* 4.0 13.7 + - + -
811A THR* 4.5 11.7 - - + -
812A LEU 3.3 15.3 - - - +
813A PHE* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 4.2 23.3 - - - +
144A GLU* 3.0 47.1 + - + +
767A GLY 3.9 4.7 - - - +
768A SER* 4.6 2.5 - - - -
785A THR* 3.7 12.4 + - + -
786A VAL* 1.3 73.6 - - - +
788A PHE* 1.3 59.8 + - - +
810A TYR* 3.5 18.3 - - + -
812A LEU* 2.9 65.9 + - + +
814A ASP* 2.9 39.9 + - - -
832A GLU* 3.7 12.6 + - - +
839A TYR* 3.3 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LEU* 6.3 3.4 - - + -
704A THR 5.0 1.6 - - - -
705A TYR* 4.0 34.3 - + + -
766A ARG* 3.6 1.2 - - - +
767A GLY* 2.9 34.7 + - - +
768A SER* 4.0 19.3 - - - -
769A VAL* 4.3 13.9 - - + -
786A VAL* 4.3 15.9 - - + -
787A ARG* 1.3 75.0 - - - +
789A ALA* 1.3 63.0 + - - +
790A PRO* 3.9 14.6 - - + -
810A TYR* 3.3 15.2 + - - +
811A THR* 4.1 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ASP 3.3 14.4 - - - +
766A ARG* 3.6 12.3 - - + -
788A PHE* 1.3 78.7 - - - +
790A PRO* 1.3 72.8 - - - +
808A PRO 4.2 2.8 - - - +
809A LYS* 3.1 23.6 - - - +
810A TYR* 3.1 36.6 + - + +
----------------------------------------------------------
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