Contacts of the strand formed by residues 709 - 715 (chain v) in PDB entry 6FF7
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 GLN 709 (chain v).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645v MET* 4.5 17.3 - - - +
646v GLY 5.6 2.0 - - - +
705v ARG* 3.3 8.6 - - - +
706v MET 2.9 30.8 + - - +
707v GLN* 3.6 2.1 - - + -
708v GLY* 1.3 81.3 - - - +
710v GLU* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 710 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643v VAL* 5.8 5.3 - - + +
644v GLU 4.7 14.8 + - - +
645v MET* 4.0 22.0 - - - +
703v ARG* 5.8 4.7 - - + -
704v VAL 3.2 13.9 - - - +
705v ARG* 4.1 4.5 - - + +
706v MET 5.2 0.2 - - - -
709v GLN* 1.3 79.9 - - - +
711v ALA* 1.3 65.4 + - - +
723v TYR* 5.7 0.5 - - - -
724v SER 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 711 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643v VAL* 5.4 8.9 - - - +
645v MET* 5.8 1.6 - - - -
703v ARG* 3.4 6.9 - - - +
704v VAL* 2.9 34.8 + - + +
705v ARG* 4.8 0.2 - - - +
706v MET* 5.7 8.3 - - + +
710v GLU* 1.3 76.8 - - - +
712v VAL* 1.3 62.8 + - - +
721v LEU* 6.3 1.8 - - + -
722v SER 3.7 14.6 - - - +
723v TYR* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 712 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641v CYS* 5.2 13.7 - - + -
643v VAL* 5.2 10.3 - - + -
665v ASN* 5.8 5.4 - - + -
701v LEU* 5.6 2.9 - - + -
702v PHE 3.5 8.7 - - - +
703v ARG* 4.8 0.7 - - - +
704v VAL* 6.2 0.4 - - - -
711v ALA* 1.3 77.5 - - - +
713v LEU* 1.3 61.8 + - - +
714v ALA* 3.9 2.5 - - + +
720v TRP 4.0 0.3 - - - +
721v LEU* 3.5 3.3 - - - +
722v SER* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 713 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700v LYS 3.1 5.5 - - - +
701v LEU* 4.3 1.1 - - - -
702v PHE* 2.9 37.3 + - - +
704v VAL* 5.4 6.9 - - + +
711v ALA 4.3 0.2 - - - -
712v VAL* 1.3 71.9 - - - +
714v ALA* 1.3 59.8 + - - +
715v MET* 4.9 3.3 - - + +
719v SER* 6.1 3.6 - - - -
720v TRP 3.6 7.0 - - - +
721v LEU* 4.3 9.4 - - + +
742v ALA* 4.4 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 714 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672v VAL* 5.2 14.4 - - + -
699v VAL* 5.3 7.2 - - + -
700v LYS 3.2 7.4 - - - +
701v LEU* 4.2 11.4 - - + +
712v VAL* 3.9 3.9 - - + -
713v LEU* 1.3 71.2 - - - +
715v MET* 1.3 59.3 + - - +
716v SER* 4.3 1.0 + - - -
718v ARG 4.4 0.5 - - - +
719v SER* 3.8 0.4 - - - -
720v TRP* 2.9 43.3 + - + +
722v SER* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 715 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698v PRO 4.1 1.6 - - - +
699v VAL* 2.9 32.1 - - - +
700v LYS* 2.9 24.4 + - + +
713v LEU* 4.9 4.0 - - + +
714v ALA* 1.3 73.6 - - - +
716v SER* 1.3 58.2 + - - +
718v ARG 4.3 2.2 - - - -
719v SER* 4.3 12.6 - - - +
739v LEU 6.2 0.9 - - - +
740v GLU* 5.3 8.1 - - - +
741v PHE 5.2 14.6 - - - +
742v ALA* 6.1 2.9 - - + -
----------------------------------------------------------
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