Contacts of the strand formed by residues 867 - 874 (chain B) in PDB entry 3PT6
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 TYR 867 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B LEU* 4.4 15.1 - - + +
779B LEU* 3.4 40.1 - - + +
814B PRO 4.1 16.8 - - - -
815B LEU* 3.5 26.9 - - + +
817B LEU* 4.1 23.1 - - + -
835B VAL* 4.7 12.6 - - + -
836B LYS 3.5 15.2 - - - +
837B VAL* 3.3 14.6 - - + -
838B ILE 2.8 22.4 + - - -
866B THR* 1.3 82.5 + - - +
868B PHE* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 868 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B ASP* 3.6 22.4 - - - -
815B LEU* 3.1 25.0 + - + -
816B GLU* 3.4 41.2 - - + -
817B LEU* 2.9 23.8 + - - +
837B VAL* 4.2 4.7 - - - +
838B ILE* 3.0 27.1 - - + +
840B LYS* 3.8 42.8 - - + -
863B ASP* 6.6 0.2 - - + -
866B THR 3.9 10.8 - - - +
867B TYR* 1.3 75.7 - - - +
869B PHE* 1.3 64.2 + - - +
870B GLN* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 869 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ARG* 4.2 28.5 - - - -
800B PHE* 3.9 20.9 - + + -
817B LEU* 3.4 24.2 - - + +
818B PHE* 4.5 2.2 - - - +
819B LEU* 3.6 39.7 - - + -
837B VAL* 4.1 4.7 - - + -
838B ILE 2.8 15.5 + - - -
839B TYR* 3.3 46.1 - + + -
840B LYS 2.9 23.0 + - - -
868B PHE* 1.3 76.7 - - - +
870B GLN* 1.3 69.1 + - - +
871B LEU 4.6 1.3 - - - -
883B PRO* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 870 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B GLU* 2.8 28.7 - - - +
817B LEU 4.3 2.0 + - - -
839B TYR* 4.0 6.4 + - - -
840B LYS* 3.3 50.3 + - + +
841B ALA 5.8 0.4 - - - -
842B PRO* 5.8 2.2 - - + +
868B PHE* 4.3 4.7 - - + -
869B PHE* 1.3 74.3 - - - +
871B LEU* 1.3 75.0 + - + +
883B PRO* 2.9 28.6 - - - +
1291B VAL* 3.4 21.4 - - - +
1292B ARG* 4.8 3.6 + - - +
1294B GLY* 4.1 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 871 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B PHE* 3.4 25.7 - - + -
819B LEU* 3.2 21.3 + - - +
869B PHE* 4.6 0.9 - - - -
870B GLN* 1.3 92.7 - - + +
872B TRP* 1.3 60.1 + - - +
873B TYR 4.1 0.2 - - - -
880B PHE* 3.8 20.9 - - + +
881B GLU* 3.0 38.1 - - - +
882B SER* 3.3 11.4 - - - +
883B PRO* 4.0 4.5 - - - -
1291B VAL* 4.1 20.2 - - + -
1294B GLY 4.7 7.6 - - - +
1295B TYR 3.5 24.7 - - - +
1296B GLN* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 872 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B HIS* 4.1 19.3 - + - -
819B LEU* 3.1 42.6 - - + -
820B VAL* 4.1 0.9 - - - -
821B GLY* 3.6 25.7 - - - +
871B LEU* 1.3 73.1 - - - +
873B TYR* 1.3 73.9 + - - +
874B ASN* 4.2 6.5 - - + +
879B ARG 3.1 4.5 - - - +
880B PHE* 4.4 1.8 - - - -
881B GLU* 2.8 48.8 + - + +
882B SER 4.8 1.1 - - - +
883B PRO* 4.6 9.4 - - + -
884B PRO* 3.8 19.3 - - + -
898B LEU* 4.0 26.9 - - + -
899B SER* 4.3 7.9 - - - -
902B ARG* 4.5 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 873 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B CYS* 4.1 13.0 - - + -
805B ASP 4.6 3.2 + - - -
806B THR* 3.2 33.7 - - + -
807B VAL* 3.5 10.4 + - + +
818B PHE* 3.8 22.7 - - + -
819B LEU 2.8 11.2 + - - +
820B VAL* 3.3 29.4 - - + +
871B LEU 4.1 1.2 + - - -
872B TRP* 1.3 74.9 + - - +
874B ASN* 1.3 71.7 + - - +
875B GLN* 3.7 30.0 + - + +
878B ALA* 3.6 13.9 - - - -
879B ARG 3.4 7.9 - - - -
880B PHE* 3.7 29.4 - + + +
1353B PHE* 3.4 28.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 874 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B VAL* 5.4 0.4 - - - -
872B TRP* 3.7 10.0 + - + +
873B TYR* 1.3 72.8 - - - +
875B GLN* 1.3 61.5 + - - +
876B GLU* 3.3 6.1 + - - +
877B TYR* 3.1 43.0 + - - +
878B ALA* 2.9 25.8 + - - -
879B ARG* 2.8 32.7 + - + +
881B GLU* 5.1 6.1 + - - +
----------------------------------------------------------
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