Contacts of the strand formed by residues 726 - 729 (chain C) in PDB entry 6VVT
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 ILE 726 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C HIS 4.9 0.4 - - - -
721C ASN* 4.5 1.1 - - - -
724C ASP 3.9 4.9 - - - +
725C ALA* 1.3 81.1 - - - +
727C ILE* 1.3 69.6 + - - +
728C LEU* 3.6 23.1 - - + -
876C LEU* 4.4 19.3 - - + +
877C ALA* 6.0 0.4 - - - -
883C LYS* 5.2 1.6 - - - -
884C GLY* 3.7 26.2 - - - +
885C VAL 2.9 13.0 + - - +
886C ILE* 3.4 7.2 - - + -
887C GLY* 2.6 29.3 + - - -
888C LYS 3.4 3.1 + - - +
906C ILE* 4.3 6.1 - - + -
907C ILE 4.1 4.7 - - - +
908C LEU* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 727 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C TRP* 3.5 20.9 - - + +
720C HIS* 3.7 17.5 - - + +
721C ASN* 3.2 29.2 - - + +
726C ILE* 1.3 75.1 - - - +
728C LEU* 1.3 64.8 + - - +
888C LYS* 3.1 32.8 - - + +
890C LEU* 3.8 16.2 - - + -
906C ILE* 3.2 5.7 - - - +
907C ILE* 3.0 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 728 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ILE* 3.6 16.2 - - + -
727C ILE* 1.3 80.6 - - - +
729C SER* 1.3 63.8 + - - +
732C LEU* 3.7 22.4 - - + -
738C LEU* 4.3 0.2 - - + -
870C ILE* 3.8 15.9 - - + -
876C LEU* 4.0 13.2 - - + -
886C ILE* 3.3 40.6 - - + -
888C LYS 3.1 5.5 + - - -
889C ILE* 3.2 15.6 - - + -
890C LEU 3.0 25.1 + - - -
895C MET* 3.8 5.3 - - - +
905C ASP 3.3 3.4 - - - -
906C ILE* 3.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 729 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C LEU* 1.3 74.6 - - - +
730C ASN* 1.3 61.6 + - - +
731C ARG* 2.8 22.1 + - - -
732C LEU* 3.1 20.7 + - - +
733C VAL 4.4 0.3 + - - -
889C ILE* 3.9 3.5 - - - +
892C VAL* 4.9 10.1 - - - -
895C MET* 3.2 21.0 - - - +
903C PRO* 5.0 1.2 - - - +
904C VAL 2.3 31.8 + - - -
905C ASP* 2.7 20.3 + - - -
----------------------------------------------------------
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