Contacts of the strand formed by residues 835 - 841 (chain B) in PDB entry 5GJE
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 PRO 835 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B THR* 4.2 20.9 - - + -
809B ASP 5.1 0.8 - - - +
810B LEU* 3.9 20.8 - - - +
813B ASN* 3.7 34.1 + - - +
814B LEU* 4.3 2.0 - - - +
815B ILE* 4.6 2.2 - - + -
832B LEU* 3.3 39.0 - - + +
833B PRO 3.8 1.8 - - - -
834B HIS* 1.3 93.9 + - - +
836B PHE* 1.3 59.2 + - - +
847B TRP* 4.4 4.7 - - + -
848B THR 3.3 10.5 - - - +
849B ASP* 3.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ARG* 3.4 25.8 - - - -
767B TRP* 5.0 2.5 - + - -
794B ASN* 3.0 23.2 + - - +
795B GLY 4.3 0.7 + - - -
808B THR* 2.9 22.2 + - - -
810B LEU* 3.6 33.4 - - + -
834B HIS* 4.4 6.7 - + - +
835B PRO* 1.3 74.9 - - - +
837B GLY* 1.3 62.8 + - - +
838B LEU 4.1 0.2 + - - -
848B THR* 2.9 17.4 + - - +
850B TRP* 3.5 36.1 - + + -
876B VAL 3.7 2.9 - - - -
877B MET* 3.0 53.6 - - + -
205C PHE* 6.2 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ASN* 4.4 3.6 - - - -
795B GLY* 5.0 1.1 - - - -
808B THR* 3.8 1.7 - - - +
836B PHE* 1.3 77.1 - - - +
838B LEU* 1.3 62.0 + - - +
847B TRP* 3.1 24.9 - - - +
848B THR* 2.9 31.9 + - - +
877B MET 4.3 12.8 - - - -
878B ASP* 5.3 2.0 - - - -
879B ILE* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B GLY* 3.6 26.4 - - - +
797B THR* 3.9 7.4 - - + +
806B TYR* 3.7 16.4 - - + -
807B TRP* 3.5 43.1 - - - +
808B THR* 3.9 7.6 - - + +
815B ILE* 4.0 18.4 - - + -
836B PHE 4.1 0.2 + - - -
837B GLY* 1.3 74.5 - - - +
839B THR* 1.3 71.3 + - - +
845B ILE* 4.2 13.2 - - + -
846B TYR 3.2 22.2 - - - +
847B TRP* 3.7 15.0 - - + -
878B ASP* 4.9 1.8 + - - +
879B ILE* 3.5 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LEU* 4.5 1.3 - - + -
797B THR* 3.9 17.7 + - - -
806B TYR* 6.5 0.2 - - - -
838B LEU* 1.3 80.0 - - - +
840B GLN* 1.3 63.1 + - - +
845B ILE* 3.4 6.1 - - - +
846B TYR* 2.7 53.4 + - + +
879B ILE* 3.9 22.9 - - + -
880B LEU* 3.7 7.8 - - - +
881B VAL* 3.3 34.7 + - + +
886B ARG* 4.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B THR* 4.1 13.1 + - + +
799B ASP* 3.1 45.3 + - + +
800B TYR 4.7 0.4 - - - +
806B TYR* 4.5 9.0 - - + -
839B THR* 1.3 80.7 + - - +
841B TYR* 1.3 68.8 + - - +
842B GLN 3.2 24.8 + - - +
844B TYR 3.4 11.3 - - - +
845B ILE* 3.9 14.4 - - + +
846B TYR* 4.5 1.6 - - - -
860B LYS* 3.6 7.0 - - - +
881B VAL* 3.5 11.4 - - - +
886B ARG* 3.1 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ALA* 3.5 26.5 + - + +
647B LEU* 4.2 20.9 - - + -
840B GLN* 1.3 81.5 - - - +
842B GLN* 1.3 110.1 + - + +
843B ASP 3.1 2.3 + - - -
844B TYR* 3.1 21.1 + - - +
846B TYR* 4.4 10.9 + - + -
881B VAL* 3.7 26.7 - - + -
883B HIS* 3.4 27.1 + + + -
885B SER* 3.3 24.0 + - - -
886B ARG* 4.4 10.1 - - - -
----------------------------------------------------------
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