Contacts of the strand formed by residues 876 - 879 (chain A) in PDB entry 2X5Y
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 876 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A TYR* 4.1 17.9 - - + +
819A TYR* 3.7 33.4 - - + -
820A PHE 3.3 10.1 - - - +
826A TYR* 3.4 44.6 - - + +
868A VAL* 3.2 30.5 - - - +
869A ASP* 3.3 18.8 + - + +
874A PRO 3.9 0.2 - - - -
875A SER* 1.3 84.0 - - - +
877A PHE* 1.3 63.4 + - - +
878A VAL* 4.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LYS* 4.5 13.7 - - + -
785A LEU* 3.7 39.9 - - + -
818A ILE 3.3 2.8 - - - +
819A TYR* 3.7 0.2 - - - -
820A PHE* 2.9 38.2 + - + +
822A LYS* 4.7 4.7 - - + -
847A VAL* 3.5 31.4 - - + -
850A PHE* 4.2 15.7 - + - -
866A SER* 4.4 4.7 - - - -
867A CYS 3.4 3.1 - - - +
868A VAL* 3.5 22.9 - - + -
874A PRO* 3.7 37.9 - - + -
875A SER 4.6 4.0 - - - -
876A VAL* 1.3 75.0 - - - +
878A VAL* 1.3 62.5 + - - +
879A ILE* 3.9 6.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A TYR* 3.9 21.5 - - + +
815A GLY 3.9 7.4 - - - +
817A GLY* 3.6 33.2 - - - +
818A ILE 3.3 2.9 - - - +
819A TYR* 3.6 34.5 - - + -
866A SER* 3.4 9.5 - - - -
867A CYS* 2.7 42.6 + - + +
876A VAL* 4.5 2.0 - - + -
877A PHE* 1.3 73.5 - - - +
879A ILE* 1.3 62.4 + - - +
880A PHE* 3.6 20.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A GLY* 3.4 1.6 - - - -
818A ILE* 2.9 39.8 + - + +
820A PHE* 3.8 20.6 - - + -
845A VAL* 3.6 31.0 - - + -
846A LEU 4.0 10.8 - - - +
847A VAL* 4.5 4.3 - - + -
865A ASP 5.2 1.1 - - - -
866A SER* 3.7 26.2 - - - -
877A PHE* 4.3 5.4 - - + +
878A VAL* 1.3 75.7 - - - +
880A PHE* 1.3 65.0 + - - +
881A GLN 3.4 23.3 - - - +
884A GLN* 3.9 14.6 - - + +
885A VAL* 3.8 14.6 - - + -
----------------------------------------------------------
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