Contacts of the strand formed by residues 721 - 727 (chain D) in PDB entry 2JDQ
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 LYS 721 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LYS* 4.8 20.3 - - - +
509B GLU* 4.2 12.1 + - - -
697D LEU* 3.6 31.0 - - + +
704D TYR* 3.5 56.9 + - + +
716D LEU* 4.4 2.5 - - - +
719D GLY 5.2 3.1 - - - +
720D GLU* 1.3 87.1 - - - +
722D ALA* 1.3 63.4 + - - +
733D LEU* 4.0 13.7 - - + -
734D VAL 3.3 7.2 - - - +
735D MET* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 722 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704D TYR* 4.5 7.6 - - - +
708D LEU* 3.6 23.8 - - + -
713D LEU* 5.1 0.2 - - + -
716D LEU* 3.6 28.0 - - + +
721D LYS* 1.3 78.1 - - - +
723D ASN* 1.3 62.0 + - - +
733D LEU* 3.5 8.2 - - - +
734D VAL* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 723 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700D GLU* 3.4 19.5 - - + +
701D ASP 3.0 43.1 + - - -
702D ARG 4.3 0.2 - - - +
704D TYR* 3.9 8.5 + - - +
705D GLY 2.8 25.0 + - - +
706D PRO 4.1 1.4 + - - +
707D ALA* 3.9 11.4 - - - +
708D LEU* 2.7 37.0 + - - +
722D ALA* 1.3 74.3 - - - +
724D VAL* 1.3 56.7 + - - +
731D VAL* 3.9 13.7 - - + -
732D VAL 3.4 3.1 - - - -
733D LEU* 3.5 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 724 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D ALA* 4.3 0.2 - - - -
708D LEU 3.5 11.4 - - - +
709D SER 3.9 10.3 - - - +
710D ILE* 4.3 5.8 - - + +
713D LEU* 3.6 36.3 - - + -
722D ALA 3.9 0.4 - - - +
723D ASN* 1.3 76.5 - - - +
725D LEU* 1.3 63.2 + - - +
726D ILE* 3.2 22.9 + - + +
731D VAL* 3.2 6.4 - - - +
732D VAL 2.8 33.5 + - - +
734D VAL* 3.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 725 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D ALA* 3.9 10.7 - - + +
708D LEU 3.0 17.8 + - - +
709D SER* 5.3 2.4 - - - -
710D ILE* 4.7 12.1 + - - +
724D VAL* 1.3 74.0 - - - +
726D ILE* 1.3 62.8 + - - +
727D GLY* 3.2 30.7 - - - +
728D GLN 3.6 12.8 - - - +
729D GLY* 4.5 1.6 - - - -
730D ASP 3.9 2.7 - - - +
731D VAL* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 726 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D LEU* 3.8 43.3 - - + -
696D ILE* 5.7 2.0 - - + -
710D ILE* 4.8 11.9 - - + +
724D VAL* 3.9 18.4 - - + -
725D LEU* 1.3 71.9 - - - +
727D GLY* 1.3 57.0 + - - +
730D ASP* 2.9 25.2 + - - +
732D VAL* 3.4 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 727 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725D LEU* 3.2 16.3 - - - +
726D ILE* 1.3 80.0 - - - +
728D GLN* 1.3 79.2 + - - +
730D ASP* 2.7 17.5 + - - +
----------------------------------------------------------
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