Contacts of the strand formed by residues 895 - 906 (chain B) in PDB entry 1GKU
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 895 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B LEU* 3.2 4.4 - - - -
768B ARG* 2.6 83.6 + - + +
769B THR 4.3 9.4 - - - -
770B PRO* 4.5 13.9 - - + -
893B ARG 3.5 0.8 + - - -
894B PRO* 1.3 74.4 - - - +
896B LYS* 1.3 70.9 + - - +
897B VAL* 4.5 8.3 - - + -
919B ALA* 4.6 2.0 - - + -
920B GLU 3.2 13.7 - - - +
921B GLY* 4.1 11.9 - - - -
923B ALA* 4.5 5.8 - - + -
924B TYR* 3.9 30.1 - + + +
929B ALA* 4.4 16.4 - - + -
930B VAL* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B GLU* 3.6 37.3 + - + +
766B GLU 3.0 7.0 - - - +
767B LEU* 3.4 32.1 - - + -
895B PHE* 1.3 77.3 - - - +
897B VAL* 1.3 62.6 + - - +
919B ALA* 3.3 2.4 - - - -
920B GLU* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B GLU* 3.3 4.7 - - - -
766B GLU* 2.7 42.7 + - + +
768B ARG* 4.2 18.8 - - - +
895B PHE* 4.5 3.6 - - + -
896B LYS* 1.3 74.4 - - - +
898B VAL* 1.3 61.3 + - - +
899B VAL* 3.8 25.3 + - + -
916B ILE* 3.1 34.1 - - + -
918B ARG 3.0 17.9 - - - +
919B ALA* 3.9 13.5 - - + -
930B VAL* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 898 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B GLU* 5.9 0.7 - - + -
764B ARG 3.5 12.3 - - - +
765B GLU* 4.8 15.9 - - + +
897B VAL* 1.3 74.1 - - - +
899B VAL* 1.3 58.3 + - - +
900B LYS* 4.2 29.6 - - + -
916B ILE* 3.4 1.7 - - - -
917B VAL* 2.6 38.8 + - + +
918B ARG* 2.6 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B GLU* 3.4 3.5 - - - -
764B ARG* 2.8 71.5 + - + +
766B GLU* 4.2 14.8 - - - +
768B ARG* 5.0 4.9 - - - +
897B VAL* 3.8 23.3 - - + -
898B VAL* 1.3 71.2 - - - +
900B LYS* 1.3 64.0 + - - +
901B LYS 4.7 0.2 - - - +
914B GLU* 4.1 24.5 - - + +
915B ARG 4.2 4.7 - - - +
916B ILE* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B GLU 3.9 4.0 - - - +
763B GLU* 3.6 32.0 + - + +
898B VAL* 3.9 18.1 + - + -
899B VAL* 1.3 77.3 - - - +
901B LYS* 1.3 63.4 + - - +
902B TYR* 3.5 17.6 - - + +
914B GLU* 4.4 0.4 - - - -
915B ARG* 3.3 34.5 + - - +
917B VAL* 3.3 22.2 - - + +
935B GLU* 2.6 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 901 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B LEU* 3.9 2.6 - - - -
761B VAL* 3.4 50.2 + - + +
762B GLU* 3.3 31.0 + - + +
764B ARG* 5.5 0.9 - - - +
899B VAL* 4.1 2.6 + - + +
900B LYS* 1.3 73.1 - - - +
902B TYR* 1.3 64.9 + - - +
912B GLU* 3.5 25.3 + - + +
913B GLU 3.3 6.5 - - - +
914B GLU* 3.4 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 902 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ILE* 3.8 13.0 - - + -
759B LYS 3.4 20.0 - - - -
760B LEU* 4.3 4.5 - - + -
761B VAL* 3.6 4.3 - - - +
900B LYS* 3.5 33.7 - - + +
901B LYS* 1.3 75.6 - - - +
903B SER* 1.3 61.0 + - - +
904B ILE* 4.7 3.4 - - + -
911B ALA 3.9 0.6 - - - +
912B GLU* 3.2 6.6 - - - +
913B GLU* 3.0 33.9 + - + +
915B ARG* 4.1 10.1 - - + -
917B VAL* 5.0 0.2 - - + -
935B GLU* 3.1 25.7 + - - +
936B LEU* 2.9 75.3 + - + -
938B THR* 4.3 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 903 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B THR 3.4 0.5 - - - +
758B ILE* 3.6 1.0 - - - -
759B LYS* 3.0 55.8 + - - +
761B VAL* 3.2 22.2 - - - -
902B TYR* 1.3 72.5 - - - +
904B ILE* 1.3 63.0 + - - +
905B GLU* 4.3 5.5 + - - -
910B THR* 5.3 1.6 - - - -
911B ALA 3.3 7.8 + - - -
912B GLU* 4.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 904 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B LEU* 3.5 36.1 - - + -
747B LEU* 5.1 2.5 - - + -
756B LEU* 4.3 12.8 - - + -
757B THR 3.1 7.0 - - - +
758B ILE* 3.9 23.1 - - + -
902B TYR* 4.7 2.9 - - + +
903B SER* 1.3 82.2 + - - +
905B GLU* 1.3 75.3 + - - +
906B PHE* 4.1 13.3 - - + -
909B LYS 3.8 0.7 - - - +
910B THR* 3.0 7.4 - - - -
911B ALA* 2.7 45.2 + - + +
913B GLU* 5.0 6.3 - - + +
936B LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 905 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ASP 3.9 0.5 - - - +
756B LEU* 2.8 8.3 - - - +
757B THR* 2.6 53.9 + - + +
759B LYS* 3.0 29.4 + - - +
903B SER* 4.3 4.9 + - - -
904B ILE* 1.3 75.1 - - - +
906B PHE* 1.3 61.3 + - - +
908B GLY 5.2 0.9 - - - +
909B LYS 3.7 3.4 - - - +
910B THR* 2.9 42.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 906 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B LEU* 4.3 25.1 - - + -
748B GLU 4.3 7.4 - - - -
749B HIS* 3.6 35.2 - + + -
754B PHE* 4.2 11.4 - - + -
755B ASP 3.9 5.8 - - - -
756B LEU* 3.9 14.8 - - + -
904B ILE* 4.1 14.4 - - + -
905B GLU* 1.3 77.9 - - - +
907B ASP* 1.3 68.5 + - - +
908B GLY 3.2 2.6 - - - +
909B LYS* 2.9 67.5 + - + +
910B THR 4.5 0.4 - - - -
911B ALA* 4.3 21.5 - - + -
----------------------------------------------------------
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