Contacts of the strand formed by residues 835 - 839 (chain B) in PDB entry 3ZNS
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 835 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B VAL* 4.1 2.2 - - - +
658B LYS 4.1 0.2 + - - -
659B ASN* 3.2 11.1 - - + +
660B GLY 2.9 24.1 + - - +
794B VAL* 3.4 15.7 - - + +
796B VAL* 4.3 7.0 - - + -
824B THR* 5.3 2.0 - - + -
827B LEU* 3.5 32.3 - - + +
828B MET* 3.9 16.8 - - + -
830B LEU 4.7 0.7 - - - +
833B GLY* 2.9 16.9 + - - +
834B ALA* 1.3 77.7 - - - +
836B VAL* 1.3 66.5 + - - +
837B LEU* 3.4 26.7 - - + -
859B LEU* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B VAL* 4.7 11.9 - - + +
648B LEU* 3.7 32.1 - - + -
649B ALA* 3.9 19.5 - - + +
652B VAL* 3.8 28.3 - - + -
660B GLY 3.4 2.7 - - - -
793B LEU* 4.6 5.2 - - + -
794B VAL 2.9 8.0 + - - +
795B LEU* 3.5 22.5 - - + +
796B VAL 2.9 25.8 + - - +
835B VAL* 1.3 79.6 - - - +
837B LEU* 1.3 69.5 + - - +
838B ALA* 5.4 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLY 2.8 12.4 + - - +
661B PHE* 3.4 19.5 - - + -
662B ALA* 2.7 33.5 + - - +
706B TRP* 3.8 20.0 - - + -
796B VAL* 3.2 33.0 - - + -
798B ALA* 4.0 9.0 - - + -
824B THR* 3.5 30.5 - - + +
827B LEU* 5.3 0.7 - - + -
835B VAL* 3.4 20.6 - - + -
836B VAL* 1.3 76.5 - - - +
838B ALA* 1.3 54.8 + - - +
855B CYS* 4.1 15.7 - - + -
859B LEU* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B VAL* 3.9 28.7 - - + -
661B PHE* 4.7 0.2 - - - -
662B ALA* 3.8 4.9 - - - -
664B VAL* 4.7 0.7 - - + -
684B SER* 6.0 0.2 - - - -
685B VAL* 3.7 29.4 - - + -
796B VAL 2.9 8.3 + - - +
797B SER 3.8 0.7 - - - -
798B ALA* 2.8 31.9 + - - +
836B VAL* 5.4 0.9 - - + +
837B LEU* 1.3 74.7 - - - +
839B LEU* 1.3 66.6 + - - +
840B GLU* 3.3 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ARG* 3.9 18.8 - - + +
548B ILE* 3.8 21.1 - - + +
551B ILE* 4.0 24.0 - - + -
661B PHE* 4.2 13.2 - - + -
662B ALA 3.0 20.2 + - - +
663B VAL* 4.5 2.7 - - + -
664B VAL* 3.6 36.3 - - - +
667B PRO* 4.6 4.9 - - - +
798B ALA 3.5 11.2 - - - +
800B PHE* 4.3 11.0 - - + -
838B ALA* 1.3 73.9 - - - +
840B GLU* 1.3 80.5 + - - +
841B GLY 3.5 20.9 - - - +
848B ILE* 5.6 2.2 - - + -
----------------------------------------------------------
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