Contacts of the strand formed by residues 721 - 728 (chain A) in PDB entry 4A9C
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 VAL 721 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE 4.1 0.2 - - - +
429A GLY* 3.4 0.2 - - - -
430A THR* 2.8 50.9 + - + +
445A TRP* 3.0 7.6 + - - -
657A PHE* 4.3 5.4 - - + -
660A THR* 3.6 28.5 - - + -
690A ASP* 3.6 30.1 - - + +
692A ILE* 3.9 17.9 - - + -
707A TYR* 3.9 18.8 - - + -
708A GLY 3.3 13.7 - - - +
709A CYS* 4.2 1.3 - - + -
719A SER 3.8 0.9 - - - +
720A PRO* 1.3 72.0 - - - +
722A PHE* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 3.8 11.4 - - + -
428A ILE 3.5 5.6 - - - -
445A TRP* 3.7 22.4 - - + +
448A SER* 3.5 44.6 - - - +
449A LYS 3.4 24.2 - - - -
453A LYS 3.8 11.7 - - - -
454A THR* 4.0 7.9 - - + -
692A ILE* 3.6 4.0 - - - +
706A SER* 4.1 4.3 - - - -
707A TYR* 3.4 10.4 - - - -
708A GLY* 2.9 57.2 + - - +
709A CYS 3.4 22.4 - - - -
710A THR* 3.8 11.4 - - + -
720A PRO 4.8 0.2 - - - -
721A VAL* 1.3 75.9 - - - +
723A GLY* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL 3.9 0.9 - - - +
427A PHE* 3.6 1.4 - - - -
428A ILE* 2.7 44.1 + - - +
692A ILE* 3.9 9.4 - - - -
706A SER* 3.3 11.2 - - - -
707A TYR* 4.5 4.3 - - - -
722A PHE* 1.3 77.4 - - - +
724A THR* 1.3 61.8 + - - -
725A PHE* 3.9 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A SER* 5.1 1.6 - - - -
426A VAL 3.4 4.5 - - - -
427A PHE* 3.7 17.0 - - + -
448A SER* 3.4 22.2 - - - +
455A LEU* 3.9 5.6 - - + +
464A HIS* 3.5 35.7 - - + +
704A CYS* 3.5 2.6 - - - -
705A ASN* 2.9 33.9 + - - +
706A SER* 2.7 33.7 + - - +
723A GLY* 1.3 71.0 - - - -
725A PHE* 1.3 69.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE 3.5 1.2 - - - +
425A SER* 3.4 7.6 + - - -
426A VAL* 2.9 34.6 + - + +
428A ILE* 3.7 21.1 - - + -
603A PHE* 3.6 28.5 - + + -
692A ILE* 4.1 17.0 - - + -
694A TRP* 3.4 41.1 - + - -
702A ILE* 4.3 11.2 - - + -
703A ILE 3.3 6.3 - - - +
704A CYS* 3.7 30.3 - - + -
705A ASN* 4.5 4.3 - - - +
707A TYR* 6.0 1.6 - + - -
723A GLY* 3.9 16.4 - - - -
724A THR* 1.3 77.9 - - - +
726A GLU* 1.3 60.7 + - - +
727A VAL* 3.8 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 4.7 22.8 - - + +
424A ILE 3.7 6.7 - - - +
425A SER* 5.5 3.8 - - - -
701A HIS* 3.7 14.5 + - + +
702A ILE* 3.4 4.9 - - - -
703A ILE* 2.8 45.8 + - + +
705A ASN* 3.4 29.7 + - - +
725A PHE* 1.3 69.8 - - - +
727A VAL* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.6 4.4 - - - -
424A ILE* 2.9 40.0 + - + +
426A VAL* 4.0 21.5 - - + -
555A PHE* 3.7 25.1 - - + -
601A HIS* 3.5 39.3 - - + +
603A PHE* 4.5 2.9 - - + -
701A HIS 3.5 2.0 - - - -
702A ILE* 4.3 12.3 - - + -
725A PHE* 4.0 17.7 - - + +
726A GLU* 1.3 76.4 - - - +
728A GLY* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASP 3.4 9.0 - - - -
423A MET* 4.1 10.5 - - - -
553A THR* 3.9 10.7 + - - +
601A HIS* 4.3 4.0 + - - -
701A HIS* 3.0 28.0 + - - +
727A VAL* 1.3 81.5 - - - +
729A VAL* 1.3 61.8 + - - +
730A THR* 5.8 0.8 - - - +
----------------------------------------------------------
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