Contacts of the strand formed by residues 777 - 782 (chain F) in PDB entry 6X34
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 777 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650F VAL* 2.9 25.9 + - - +
686F TRP* 3.2 40.7 - - + -
687F ALA 3.7 2.5 - - - -
688F LEU* 4.3 18.4 - - + -
712F TYR 4.0 18.2 - - - -
714F TYR* 4.1 28.5 - + - -
750F LEU* 5.3 13.9 - - + +
771F PHE* 5.0 9.4 - + - -
772F ASN 4.8 4.7 - - - -
773F LEU* 3.5 36.8 - - + -
774F ASN 5.0 0.7 - - - -
775F GLY* 3.8 9.0 - - - -
776F LEU* 1.3 90.5 - - - +
778F PHE* 1.3 60.4 + - - +
779F PRO* 4.5 0.2 - - - +
1470F ARG* 5.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 778 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645F ARG* 3.2 61.0 - - + -
646F PRO 5.3 1.1 - - - +
648F ILE 3.9 16.6 - - - +
649F PHE* 4.8 11.7 - + + -
650F VAL* 5.4 1.3 - - - +
686F TRP* 3.4 3.9 - - - -
687F ALA* 2.9 49.4 + - + -
688F LEU 3.2 30.7 - - - -
689F THR* 3.5 11.2 - - - -
692F TYR* 5.2 1.3 - + - -
776F LEU* 5.1 4.0 - - + -
777F PHE* 1.3 75.8 - - - +
779F PRO* 1.3 75.0 - - + +
780F VAL* 4.7 1.8 - - + -
826F ILE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 779 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645F ARG* 3.5 9.5 - - - +
646F PRO* 3.3 42.8 - - + +
648F ILE* 4.6 17.7 - - + +
650F VAL* 6.1 2.5 - - + -
664F PHE* 3.5 36.8 - - + -
685F GLY 3.5 6.7 - - - +
686F TRP* 3.6 20.4 - - + -
778F PHE* 1.3 87.9 - - + +
780F VAL* 1.3 57.9 + - - +
791F PHE* 4.4 9.2 - - + -
811F CYS* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 780 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643F SER* 5.1 3.4 - - - -
644F ILE 3.4 12.8 - - - +
645F ARG* 4.9 0.2 - - + -
684F VAL* 3.3 6.4 - - - +
685F GLY 2.7 37.1 + - - +
687F ALA* 4.2 19.1 - - + -
692F TYR* 5.0 5.8 - - + -
707F VAL* 3.8 19.9 - - + +
778F PHE* 3.7 7.4 + - + +
779F PRO* 1.3 76.0 - - - +
781F VAL* 1.3 62.7 + - - +
791F PHE* 5.9 1.6 - - - -
826F ILE* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 781 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643F SER* 3.3 5.8 - - - -
644F ILE* 3.2 42.5 + - + +
666F VAL* 6.2 2.9 - - + -
682F LEU* 5.4 5.4 - - + -
683F ARG 3.7 12.1 - - - +
684F VAL* 4.2 16.4 - - + -
707F VAL* 4.7 0.4 - - - -
780F VAL* 1.3 77.4 - - - +
782F SER* 1.3 72.0 + - - +
783F PHE* 4.4 7.2 + - + -
789F VAL* 4.6 28.7 - - + -
791F PHE* 4.9 18.4 - - + -
1628F VAL* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 782 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641F VAL* 5.7 0.7 - - - -
642F THR 3.5 17.7 + - - -
643F SER* 4.1 0.9 - - - -
681F HIS* 3.6 24.2 - - - +
682F LEU* 3.6 6.9 - - - +
683F ARG* 3.0 26.4 + - - +
692F TYR* 3.9 4.0 + - - -
706F GLY* 4.2 4.3 - - - -
707F VAL* 3.3 38.9 + - - +
781F VAL* 1.3 76.9 + - - +
783F PHE* 1.3 62.4 + - - +
----------------------------------------------------------
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