Contacts of the strand formed by residues 858 - 861 (chain C) in PDB entry 6VSB
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 LEU 858 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B PHE* 4.8 6.2 - - - -
734C THR* 4.9 1.8 - - - +
735C SER 3.7 5.6 - - - +
736C VAL* 3.6 29.6 - - + -
741C TYR* 5.0 6.5 - - + -
853C GLN 5.5 1.6 - - - +
854C LYS* 3.1 36.4 - - + +
855C PHE 4.2 10.3 + - - +
856C ASN* 3.1 11.5 - - - +
857C GLY* 1.3 83.6 + - - +
859C THR* 1.3 65.6 + - - +
959C LEU* 4.1 26.0 - - + -
962C LEU* 4.1 13.2 - - + -
963C VAL* 3.5 32.8 - - + -
1007C TYR* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 859 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B GLN* 4.8 16.6 + - - +
614B ASP* 4.4 11.4 + - - +
734C THR* 3.4 7.1 + - - -
735C SER* 2.8 57.9 + - - +
854C LYS* 3.5 20.3 - - - +
857C GLY 5.4 1.3 - - - +
858C LEU* 1.3 78.5 - - - +
860C VAL* 1.3 79.1 + - - +
861C LEU* 4.9 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 860 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ASP* 4.1 10.4 - - - +
732C THR* 3.8 33.7 - - + +
733C LYS 3.7 4.7 - - - +
734C THR* 4.3 4.0 - - - +
853C GLN* 5.8 8.7 - - - +
854C LYS* 3.8 15.2 + - + +
859C THR* 1.3 87.6 + - - +
861C LEU* 1.3 75.9 + - - +
862C PRO* 3.8 3.8 - - - +
955C ASN* 5.9 0.2 - - - +
959C LEU* 4.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 861 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 6.0 2.7 - - - +
613B GLN* 3.2 41.7 - - - +
732C THR* 5.5 0.2 - - - -
733C LYS* 2.6 48.5 + - + +
735C SER* 4.5 15.5 - - - -
771C ALA* 4.0 22.9 - - + -
859C THR* 4.9 6.3 - - + +
860C VAL* 1.3 87.2 - - - +
862C PRO* 1.3 76.5 - - + +
863C PRO* 3.8 2.4 - - - +
----------------------------------------------------------
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