Contacts of the strand formed by residues 720 - 728 (chain B) in PDB entry 5L73
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 HIS 720 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B TYR* 3.4 37.1 + + - -
713B VAL* 4.5 11.2 - - + +
714B TYR* 3.2 27.0 + - + -
715B SER* 5.3 0.4 - - - -
718B SER* 3.8 20.1 + - - -
719B ALA* 1.3 77.5 - - - +
721B CYS* 1.3 57.1 + - - +
722B MET 3.9 0.2 - - - -
769B LEU* 3.5 8.6 - - - +
770B LEU* 2.7 44.8 + - + +
800B ILE* 4.0 43.0 - - + +
806B GLN* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B HIS* 1.3 73.1 - - - +
722B MET* 1.3 60.4 + - - +
723B THR* 4.4 0.7 - - - -
767B ARG* 3.8 23.6 - - - -
769B LEU* 5.2 0.7 - - + -
799B SER 3.5 3.5 - - - +
800B ILE* 3.5 9.7 + - - +
802B ASN* 3.0 37.3 + - - +
804B ILE* 4.1 20.6 - - + +
809B CYS* 2.1 55.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 3.6 32.8 - - + -
720B HIS 3.9 2.2 + - - -
721B CYS* 1.3 73.3 - - - +
723B THR* 1.3 71.3 + - - +
724B PHE* 4.2 7.4 - - + -
738B VAL* 3.8 14.4 - - + -
767B ARG* 3.2 5.4 - - - +
768B VAL* 2.8 55.7 + - + +
770B LEU* 3.9 16.4 - - + -
779B VAL* 3.8 23.6 - - + -
781B PHE* 3.8 21.8 - - + -
798B ILE* 3.8 13.5 - - + -
799B SER 3.4 8.1 - - - +
800B ILE* 4.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A THR* 3.7 37.1 + - + +
721B CYS* 4.4 1.3 - - - +
722B MET* 1.3 80.4 - - - +
724B PHE* 1.3 64.0 + - - +
725B TRP* 5.4 0.5 + - - -
765B GLU* 5.2 0.7 - - - -
766B GLY 3.5 7.9 - - - -
767B ARG* 3.8 22.7 - - + -
797B ASP 3.5 2.6 + - - +
798B ILE* 3.4 1.0 - - - -
799B SER* 2.9 47.4 + - - -
802B ASN* 3.6 22.0 + - - +
804B ILE* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B MET* 4.2 8.1 - - + -
723B THR* 1.3 80.7 - - - +
725B TRP* 1.3 75.7 + - - +
726B TYR* 3.7 25.1 - + + -
736B LEU* 4.4 2.7 - - + -
738B VAL* 4.2 6.1 - - + -
753B TRP* 3.7 38.1 - + - -
765B GLU* 3.6 4.9 - - - +
766B GLY* 2.8 48.5 + - - -
767B ARG* 4.0 2.2 - - - -
768B VAL* 4.2 18.8 - - + -
781B PHE* 3.7 39.7 - + + -
795B VAL* 4.5 1.6 - - + -
796B ASP 4.0 5.8 - - - +
797B ASP 3.5 9.0 - - - -
798B ILE* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A THR* 3.4 37.1 + - + +
688A GLY* 4.5 5.2 - - - -
723B THR* 5.4 0.4 + - - -
724B PHE* 1.3 81.4 - - - +
726B TYR* 1.3 61.8 - - - +
763B TRP* 3.8 24.2 - - + -
764B LYS* 3.2 25.1 - - - -
765B GLU* 3.8 38.6 - - + -
795B VAL* 3.3 7.8 - - - +
796B ASP 3.0 35.5 + - - +
797B ASP* 4.0 21.4 + - + -
903B BCN 3.6 49.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B PHE* 3.7 18.4 - + + -
725B TRP* 1.3 76.0 - - - +
727B HIS* 1.3 60.9 + - - +
728B MET* 4.0 22.6 + - + -
736B LEU* 3.9 17.7 - - + -
753B TRP* 3.5 34.4 - + - -
755B ALA* 4.6 0.2 - - + -
759B GLN* 4.0 25.4 + - + -
762B HIS 4.1 0.9 - - - +
763B TRP* 3.5 5.5 - - - -
764B LYS* 2.8 67.9 + - + +
765B GLU 3.8 6.6 + - - -
766B GLY* 3.7 17.5 - - - -
794B ALA 3.2 9.9 - - - +
795B VAL* 4.5 0.4 - - + -
812B PRO 4.6 1.7 + - - -
813B ALA* 3.8 15.4 - - - +
814B HIS 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PRO* 4.3 9.4 + - + -
683B ILE* 3.7 33.1 - - + +
726B TYR* 1.3 73.7 - - - +
728B MET* 1.3 63.5 + - - +
729B SER* 3.8 26.1 + - - -
761B ASP 4.0 5.1 + - - -
762B HIS* 3.7 22.4 + - - -
763B TRP* 3.5 51.1 - + + -
792B GLY 3.3 9.4 - - - +
794B ALA* 2.9 45.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B TYR* 4.0 16.8 + - + -
727B HIS* 1.3 80.9 + - - +
729B SER* 1.3 58.0 + - - +
733B VAL* 3.9 16.4 - - + -
734B GLY 3.5 17.5 - - - +
736B LEU* 3.8 21.5 - - - +
755B ALA* 3.3 44.6 - - + +
757B GLY 3.4 17.0 - - - +
758B HIS* 3.6 2.4 - - - -
759B GLN* 2.8 38.4 + - + +
760B GLY 3.4 10.1 + - - +
762B HIS 5.0 1.0 + - - -
764B LYS* 6.3 0.2 - - - +
793B ILE* 3.9 20.0 - - + -
----------------------------------------------------------
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