Contacts of the strand formed by residues 798 - 806 (chain A) in PDB entry 4QUM
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 GLU 798 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A TRP* 4.4 1.6 - - - -
789A LEU* 3.8 31.8 - - + +
790A VAL 3.5 3.4 - - - -
791A THR* 4.1 15.4 + - + +
796A GLY 4.0 9.2 - - - +
797A GLU* 1.3 87.4 - - - +
799A HIS* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A VAL* 4.4 13.9 - - + -
733A TRP* 3.8 24.0 - + + -
736A LYS* 3.6 40.0 - - + +
737A LEU 2.7 29.6 + - - -
738A SER* 4.4 4.7 - - - -
789A LEU* 3.7 4.6 - - - -
790A VAL* 2.7 46.0 + - + +
798A GLU* 1.3 76.4 - - - +
800A THR* 1.3 75.7 + - + +
801A VAL* 3.3 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A SER* 4.2 7.8 - - - -
775A GLN* 4.7 8.0 + - - -
787A GLU* 4.1 13.5 + - - +
788A MET 3.3 10.2 + - - -
789A LEU* 4.6 9.0 - - - -
799A HIS* 1.3 91.2 + - + +
801A VAL* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A TRP* 4.8 2.5 - - + -
732A VAL* 3.9 9.4 - - + -
737A LEU 3.5 6.1 - - - +
738A SER 3.6 12.3 - - - +
740A ILE* 3.7 29.2 - - + -
786A ARG 3.8 0.2 - - - +
787A GLU* 3.6 5.3 - - - +
788A MET* 2.8 50.6 + - + +
790A VAL* 4.3 12.6 - - + -
799A HIS* 3.3 34.3 - - + +
800A THR* 1.3 73.0 + - - +
802A THR* 1.3 78.3 + - - +
803A HIS* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A SER 2.8 15.9 + - - -
739A LEU* 3.4 11.4 - - + +
740A ILE 2.9 25.5 + - - -
785A SER* 4.7 3.8 - - - +
786A ARG 3.6 5.6 - - - +
787A GLU* 2.9 30.2 + - - +
801A VAL* 1.3 78.9 - - - +
803A HIS* 1.3 61.5 + - - +
804A LEU* 4.1 12.6 - - + -
827A TYR* 5.0 1.6 - - - +
831A LEU* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A ILE* 3.5 34.1 - - + +
742A MET* 3.9 26.8 - - + +
757A TYR* 2.8 33.7 + + - -
758A TRP* 4.1 11.6 - + - -
784A VAL 3.6 1.6 - - - +
785A SER* 3.5 0.3 - - - -
786A ARG* 2.8 54.9 + - + +
788A MET* 3.7 36.0 - - + +
801A VAL* 5.3 0.7 - - + -
802A THR* 1.3 75.3 - - - +
804A LEU* 1.3 66.9 + - - +
805A GLN* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LEU* 4.2 15.0 - - + -
740A ILE 2.8 12.6 + - - +
741A VAL* 3.5 4.1 - - + +
742A MET* 2.7 34.3 + - - +
783A TYR* 4.6 3.4 - - + -
784A VAL 3.5 2.0 - - - +
785A SER* 3.6 28.0 - - - +
802A THR* 4.1 8.7 - - + -
803A HIS* 1.3 85.5 + - - +
805A GLN* 1.3 56.1 + - - +
806A TYR 4.0 0.8 + - - -
824A PHE* 3.9 28.0 - - + -
827A TYR* 3.7 32.1 - - + -
828A VAL* 4.2 15.9 - - + -
831A LEU* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A MET* 3.2 26.8 - - + +
744A THR 2.9 28.7 + - - +
745A THR* 3.7 14.1 - - - +
746A LEU* 4.3 4.6 - - - +
758A TRP* 4.1 7.5 - - - -
783A TYR* 3.1 4.5 - - - +
784A VAL* 2.8 39.7 + - + +
786A ARG* 3.2 35.7 + - - +
803A HIS* 4.2 8.2 - - + -
804A LEU* 1.3 70.8 - - - +
806A TYR* 1.3 60.8 + - - +
807A VAL* 3.4 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A MET 2.8 7.9 + - - -
743A LEU* 3.7 26.8 - - + -
744A THR* 3.5 23.9 + - - -
782A ALA* 3.5 21.7 - - + +
783A TYR* 3.7 3.8 - + + +
804A LEU 4.0 1.8 - - - -
805A GLN* 1.3 71.1 - - - +
807A VAL* 1.3 59.6 + - - +
808A ALA* 3.5 32.9 + - + +
809A TRP* 3.7 25.7 + + + +
815A PRO* 4.1 6.5 - - + +
817A ASP 3.8 6.8 + - - -
820A ASP* 3.5 12.9 - - - +
821A PHE* 3.3 29.7 + + + +
824A PHE* 3.5 49.5 - + + -
----------------------------------------------------------
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