Contacts of the strand formed by residues 893 - 901 (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 ASN 893 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B LYS 3.4 4.9 - - - -
717B GLY* 3.7 1.6 - - - -
718B ASP* 2.8 46.5 + - - +
719B LEU* 3.8 9.9 - - + +
721B LYS* 5.7 4.9 + - - +
722B GLY* 3.2 18.3 - - - +
725B GLU* 5.1 5.1 + - - -
857B VAL* 2.7 26.1 + - - +
858B ALA* 3.2 4.6 - - - -
859B LEU 2.9 24.9 + - - -
891B ILE* 3.5 2.5 - - - +
892B PRO* 1.3 88.1 - - - +
894B ILE* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 894 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714B ILE* 5.5 1.8 - - + +
715B GLU* 3.3 3.4 - - - +
716B LYS* 2.8 51.1 + - + +
719B LEU* 3.9 3.9 - - - +
859B LEU* 3.3 24.2 - - + +
885B MET* 3.6 42.4 - - + -
886B ASP* 4.9 4.5 - - + -
891B ILE* 4.0 26.5 - - + +
893B ASN* 1.3 76.7 - - - +
895B ARG* 1.3 65.3 + - - +
896B GLY 4.7 0.2 - - - +
954B HIS* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 895 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLU* 4.7 4.8 + - - -
713B LYS* 3.2 32.9 - - + +
714B ILE 3.4 3.4 - - - -
715B GLU* 3.2 38.0 + - + +
719B LEU* 3.2 28.4 - - + +
859B LEU 3.0 6.9 + - - -
860B GLU* 3.5 14.9 + - + +
861B VAL 3.1 24.1 + - - +
862B ASP* 4.1 12.0 + - - +
885B MET* 4.1 3.0 - - - +
894B ILE* 1.3 74.8 - - - +
896B GLY* 1.3 59.8 + - - +
897B THR* 3.8 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B LYS* 3.1 4.9 - - - +
714B ILE* 2.9 33.9 + - - -
861B VAL 3.3 7.4 - - - -
882B LEU* 3.9 9.7 - - - +
885B MET* 3.5 26.9 - - - -
894B ILE* 4.7 0.2 - - - +
895B ARG* 1.3 75.4 - - - +
897B THR* 1.3 62.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLU* 3.8 22.5 + - - +
712B LEU 3.0 9.2 - - - -
713B LYS* 3.6 26.9 - - + -
861B VAL 3.0 5.5 + - - -
862B ASP* 2.5 35.4 + - - +
863B HIS* 2.8 32.1 + - - -
864B TYR* 5.9 0.2 - - - -
882B LEU* 3.9 4.7 - - - -
895B ARG* 3.8 18.6 - - + +
896B GLY* 1.3 77.6 - - - -
898B GLY* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 898 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B SER 4.5 0.7 - - - +
711B GLU* 3.5 7.8 - - - +
712B LEU* 2.7 38.2 + - - +
863B HIS 3.3 7.2 - - - -
878B MET* 3.7 28.9 - - - -
882B LEU* 4.3 1.1 - - - +
897B THR* 1.3 77.3 - - - +
899B ARG* 1.3 60.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B ASN* 4.7 4.8 + - - +
707B PHE* 3.3 55.2 - - + +
708B TYR 5.2 0.2 + - - -
709B GLY 3.0 21.8 + - - -
710B SER* 3.3 13.1 - - - +
711B GLU* 3.2 41.0 - - + +
863B HIS 2.9 6.0 + - - +
864B TYR* 3.4 27.2 - - + +
865B SER 3.2 22.9 + - - -
878B MET* 3.4 4.9 - - - +
898B GLY* 1.3 72.1 - - - -
900B LEU* 1.3 65.2 + - - +
901B CYS 3.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B PHE* 3.0 8.8 - - - +
708B TYR* 2.9 65.1 + - + +
710B SER 6.2 0.7 - - - +
712B LEU* 5.8 1.6 - - + -
865B SER* 3.5 20.9 - - - +
867B ALA* 4.5 3.6 - - + -
871B ARG* 6.2 2.5 - - + -
874B SER* 3.6 26.9 - - - +
875B HIS* 3.7 41.1 - - + +
878B MET* 3.7 22.7 - - + -
899B ARG* 1.3 75.5 - - - +
901B CYS* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 901 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ILE* 3.8 30.5 - - - -
701B ALA* 3.5 23.6 - - + -
702B ILE* 4.6 0.9 - - - -
706B SER 3.5 4.5 - - - -
707B PHE* 3.9 17.5 - - - -
708B TYR* 4.4 0.2 - - - -
864B TYR* 4.2 11.0 - - - -
865B SER 2.9 24.8 + - - +
866B ASN* 4.3 2.7 - - - -
867B ALA* 3.0 28.2 + - - +
868B GLY 3.8 0.2 + - - -
899B ARG 4.7 0.4 - - - -
900B LEU* 1.3 71.0 - - - +
902B LYS* 1.3 62.4 + - - +
903B THR* 3.5 10.8 + - + +
----------------------------------------------------------
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