Contacts of the strand formed by residues 788 - 796 (chain A) in PDB entry 4FUL
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 ASP 788 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 2.7 42.6 + - - -
690A ARG* 4.8 7.9 + - - +
785A VAL* 2.8 18.8 + - + +
786A PRO 3.2 0.2 - - - -
787A TYR* 1.4 93.5 - - + +
789A PRO* 1.4 67.6 - - - +
790A GLY 3.2 4.4 + - - -
791A LEU* 3.0 31.1 + - + +
880A GLU* 5.5 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP* 4.9 0.5 - - - +
690A ARG* 3.4 35.7 - - + +
693A HIS* 3.5 41.3 - - + +
694A PHE* 3.6 18.6 - - + -
784A ARG* 3.1 39.0 + - + -
785A VAL 3.1 6.5 - - - +
788A ASP* 1.4 85.6 - - - +
790A GLY* 1.3 55.5 + - - +
791A LEU 3.5 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A HIS* 6.1 0.4 - - - -
276A GLY 4.2 0.3 - - - +
277A ARG* 3.3 23.2 - - - -
278A ASP* 3.0 44.4 + - - +
279A GLU* 4.4 9.2 - - - -
690A ARG* 4.9 2.6 - - - +
784A ARG* 4.2 1.4 + - - -
788A ASP* 3.2 3.0 + - - -
789A PRO* 1.3 79.5 - - - +
791A LEU* 1.3 59.8 + - - +
792A LYS* 3.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY 4.4 8.3 - - - +
277A ARG* 3.5 21.8 - - - +
784A ARG* 3.5 4.9 - - - -
785A VAL* 2.9 38.7 + - + -
787A TYR* 5.9 1.8 - - + -
788A ASP* 3.0 31.0 + - + +
789A PRO 3.8 2.0 - - - +
790A GLY* 1.3 77.3 - - - +
792A LYS* 1.3 66.7 + - - +
817A CYS* 4.1 13.9 - - - -
828A ILE* 3.8 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY 4.9 1.8 + - - +
730A HIS* 5.5 4.5 + - - -
731A ASP* 4.5 8.3 + - - -
734A GLN* 6.2 0.4 - - - +
782A SER* 3.4 28.9 - - - +
783A PHE* 3.5 21.7 - - - +
784A ARG* 3.7 44.0 - - - +
785A VAL* 4.7 0.2 - - - -
790A GLY 3.9 2.3 + - - +
791A LEU* 1.3 76.0 - - - +
793A ALA* 1.3 59.3 + - - +
817A CYS* 3.5 13.2 - - - -
818A ALA* 3.1 32.8 + - + +
819A ASP* 5.5 8.1 - - + +
828A ILE* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A SER* 3.2 7.4 - - - -
783A PHE* 2.8 66.1 + - + +
785A VAL* 4.2 12.4 - - + +
791A LEU 4.2 1.0 - - - -
792A LYS* 1.3 71.7 - - - +
794A GLY* 1.3 59.5 + - - +
815A PHE* 3.8 17.7 - - + -
816A LYS 3.9 3.6 - - - -
818A ALA* 3.9 1.8 - - - -
828A ILE* 4.1 8.3 - - + -
830A ILE* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A LEU* 4.5 5.2 - - - +
780A PRO 5.5 0.4 - - - +
781A GLU 4.2 13.2 - - - -
782A SER* 5.0 0.6 - - - -
783A PHE* 4.2 5.2 - - - -
793A ALA* 1.3 76.7 - - - +
795A ALA* 1.3 66.6 + - - -
796A LEU 3.9 0.2 + - - -
815A PHE* 3.4 14.8 - - - -
816A LYS* 2.6 20.6 + - - -
818A ALA* 3.7 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A GLN* 3.7 17.0 - - - +
779A LEU* 4.6 5.2 - - - -
781A GLU 4.5 5.0 + - - +
794A GLY* 1.3 71.1 - - - -
796A LEU* 1.3 64.5 + - - +
815A PHE* 3.4 1.1 - - - -
816A LYS* 2.9 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A LEU* 4.9 2.7 - - + -
771A LEU* 3.7 38.6 - - + +
774A LEU* 5.2 0.9 - - + -
775A GLN* 2.9 34.7 + - + +
779A LEU* 4.1 24.5 - - + +
794A GLY 3.9 1.0 + - - -
795A ALA* 1.3 71.9 - - - +
797A ALA* 1.3 56.8 + - - +
798A ILE* 3.3 10.5 + - + -
799A GLU* 5.1 0.3 - - - +
801A CYS* 3.6 25.8 - - - -
813A LEU* 4.3 10.5 - - + -
814A GLU 3.5 7.6 - - - +
815A PHE* 3.5 33.0 - - + -
816A LYS* 4.2 7.9 + - - -
----------------------------------------------------------
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