Contacts of the strand formed by residues 842 - 850 (chain B) in PDB entry 1VDV
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 PHE 842 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ILE* 4.3 1.1 - - - -
735B TYR* 3.4 9.0 - - - -
736B ILE* 2.9 49.2 + - + +
840B HIS* 3.3 24.2 + - + -
841B PRO* 1.3 76.5 - - - +
843B LEU* 1.3 60.3 + - - +
863B HIS* 3.9 25.4 - + + -
864B TYR 3.4 9.6 - - - -
865B SER* 3.6 13.0 - - - -
877B ILE* 4.7 11.7 - - + -
878B MET* 3.8 35.4 - - + -
881B ALA* 4.1 19.7 - - + -
918B GLN* 3.5 34.8 - - + -
922B ILE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ILE* 3.9 37.4 - - + +
699B GLU* 4.0 13.7 - - + +
702B ILE* 4.5 6.5 - - + -
733B GLU* 3.8 24.9 - - + +
734B LEU 3.4 17.7 - - - +
735B TYR* 4.3 15.9 - - + -
842B PHE* 1.3 74.7 - - - +
844B ALA* 1.3 65.5 + - - +
845B ARG* 4.2 26.9 - - - +
863B HIS* 3.7 1.2 - - - +
864B TYR* 2.9 39.4 + - + +
1295B ARG* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B GLU* 3.1 9.4 - - - +
734B LEU* 2.8 43.6 + - + +
842B PHE 4.3 0.2 - - - -
843B LEU* 1.3 77.7 - - - +
845B ARG* 1.3 64.5 + - - +
846B TYR* 4.1 2.5 - - + -
861B VAL* 4.4 5.8 - - + -
862B ASP 3.4 9.0 - - - +
863B HIS* 5.0 0.7 - - - -
864B TYR* 5.2 0.2 - - - -
922B ILE* 3.5 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B GLU* 5.8 5.3 - - - +
702B ILE* 4.4 25.8 - - - +
732B GLY 3.4 6.7 - - - +
733B GLU* 3.1 30.1 + - + +
843B LEU* 4.2 20.5 - - + +
844B ALA* 1.3 77.6 - - - +
846B TYR* 1.3 59.7 + - - +
860B GLU 4.0 0.5 - - - +
861B VAL* 3.6 1.1 - - - -
862B ASP* 2.9 44.5 + - + +
864B TYR* 4.4 20.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B VAL* 4.4 9.4 - - + +
731B SER* 3.3 7.4 + - - -
732B GLY* 2.9 63.2 + - - +
733B GLU* 3.5 14.7 + - - -
734B LEU* 4.4 5.2 - - + -
844B ALA 4.5 3.8 - - - -
845B ARG* 1.3 77.2 - - - +
847B LYS* 1.3 65.9 + - - +
848B VAL 4.8 0.2 - - - -
859B LEU* 5.1 0.4 - - + -
860B GLU 3.1 11.4 - - - +
861B VAL* 3.8 19.5 - - + -
922B ILE* 5.0 7.9 - - + -
925B ASN* 3.4 18.6 + - - -
926B TRP* 3.7 30.7 - + + -
929B GLU* 2.7 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B PHE* 3.4 47.0 - - + +
729B VAL* 3.8 15.3 - - + -
730B VAL 3.1 6.1 - - - -
731B SER* 3.3 18.4 - - - +
846B TYR* 1.3 78.3 - - - +
848B VAL* 1.3 62.5 + - - +
859B LEU* 3.6 3.6 - - - +
860B GLU* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B PHE* 4.3 2.2 - - - -
729B VAL* 3.2 4.3 - - - -
730B VAL* 2.7 58.5 + - + +
846B TYR* 4.8 0.9 - - + -
847B LYS* 1.3 75.0 - - - +
849B GLY* 1.3 68.6 + - - +
850B PHE* 3.6 5.2 - - + -
856B ILE* 4.0 20.6 - - + -
858B ALA 3.4 10.1 - - - +
859B LEU* 4.0 13.7 - - + -
926B TRP* 4.1 34.8 - - + +
930B VAL* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B PHE* 3.9 9.7 - - - -
726B ALA* 3.7 10.1 - - - -
728B ASN 3.3 7.9 - - - -
729B VAL* 4.1 8.1 - - - -
848B VAL* 1.3 72.1 - - - +
850B PHE* 1.3 63.2 + - - +
856B ILE* 3.9 3.3 - - - +
857B VAL* 2.9 28.7 + - - -
858B ALA 2.7 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ALA* 3.4 2.4 - - - +
727B ASP 3.1 4.7 + - - -
728B ASN* 2.8 62.3 + - + +
730B VAL* 3.6 23.6 - - + -
848B VAL* 3.6 17.7 - - + -
849B GLY* 1.3 74.0 - - - +
851B MET* 1.3 81.6 + - - +
854B GLY 4.5 0.9 - - - +
855B THR 3.2 19.3 - - - +
856B ILE* 4.1 10.3 - - + -
857B VAL* 4.0 3.8 - - - -
930B VAL* 3.8 30.5 - - + -
933B THR* 3.7 23.8 - - + -
934B CYS* 3.3 26.2 - - - -
----------------------------------------------------------
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