Contacts of the strand formed by residues 822 - 828 (chain B) in PDB entry 3HS0
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 822 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B PHE* 4.1 8.1 - - + -
816B ASN* 3.4 35.7 - - + +
818B VAL* 5.1 1.6 - - + -
820B GLU* 3.6 18.4 - - + +
821B ASP* 1.3 79.4 - - - +
823B TYR* 1.3 59.3 + - - +
824B VAL* 3.7 21.8 - - + -
848B PHE 4.2 0.2 - - - +
849B PRO* 3.4 5.4 - - - +
850B ILE* 3.0 42.2 + - + +
878B VAL* 3.5 33.0 - - + -
883B TRP* 4.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B PHE* 4.4 4.3 - + - -
822B ILE* 1.3 74.8 - - - +
824B VAL* 1.3 60.6 + - - +
847B GLN* 3.5 39.8 + - + +
848B PHE* 3.4 34.8 - - - -
849B PRO* 3.6 14.4 - - + -
878B VAL* 3.8 2.6 - - - +
879B GLN* 2.8 69.1 + - + +
1424C PHE* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B PHE* 3.9 4.2 - - - -
792B PHE* 4.2 12.1 - - + -
814B LEU* 3.7 17.0 - - + -
822B ILE* 3.7 30.1 - - + -
823B TYR* 1.3 80.3 - - - +
825B ARG* 1.3 61.3 + - - +
826B VAL* 4.1 3.1 - - + -
847B GLN* 3.1 6.4 - - - +
848B PHE* 3.0 62.6 + - + +
850B ILE* 3.8 14.6 - - + -
876B ALA* 5.7 0.2 - - + -
877B SER 3.4 12.1 - - - +
878B VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ASP* 3.7 23.0 + - - +
717B PHE* 3.2 57.2 - - + +
718B ILE 5.8 0.8 + - - -
824B VAL* 1.3 73.3 - - - +
826B VAL* 1.3 66.7 + - - +
827B GLU* 4.3 13.1 + - + -
845B ARG* 3.2 63.6 - - + +
846B GLN 3.1 5.8 - - - +
847B GLN* 3.8 11.6 - - + +
875B LYS 3.8 0.7 - - - +
876B ALA* 3.2 5.0 - - - +
877B SER* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B LEU* 3.8 22.4 - - + -
824B VAL* 4.1 2.5 - - + -
825B ARG* 1.3 76.9 - - - +
827B GLU* 1.3 62.4 + - - +
844B TYR 3.7 1.0 - - - +
845B ARG* 3.5 1.9 - - - -
846B GLN* 2.8 35.3 + - + +
848B PHE* 3.7 36.3 - - + -
858B VAL* 4.8 8.7 - - + -
860B PHE* 4.4 12.4 - - + -
874B ILE* 3.7 23.1 - - + -
875B LYS 3.3 12.6 - - - +
876B ALA* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ASP* 3.7 11.1 - - - +
825B ARG* 4.3 11.5 + - + -
826B VAL* 1.3 78.0 - - - +
828B LEU* 1.3 59.9 + - - +
829B LEU* 4.0 3.7 + - + +
843B ARG* 3.1 45.2 + - + +
844B TYR 3.2 11.4 - - - +
845B ARG* 3.0 47.1 + - + +
860B PHE* 5.0 2.0 - - - -
874B ILE* 3.6 8.1 - - - +
875B LYS* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B GLU* 1.3 71.5 - - - +
829B LEU* 1.3 70.0 + - - +
834B PHE* 6.4 2.5 - - + -
836B SER* 3.5 34.1 - - - +
837B ALA* 4.7 4.0 - - + +
838B SER* 2.6 33.9 + - - +
843B ARG* 3.5 8.4 - - - +
844B TYR* 3.2 12.7 + - + +
860B PHE* 3.8 39.1 - - + -
861B VAL 5.7 0.4 - - - +
862B ILE* 4.9 9.4 - - + -
872B VAL* 4.2 24.5 - - + -
873B GLU 4.0 7.6 - - - +
874B ILE* 4.3 9.0 - - + +
----------------------------------------------------------
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