Contacts of the strand formed by residues 707 - 714 (chain q) 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 MET 707 (chain q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700q SER 3.9 0.2 - - - +
701q TYR* 3.5 2.8 - - - -
702q ASN* 3.0 30.8 + - + +
705q THR* 3.5 11.8 - - - +
706q GLY* 1.3 80.2 - - - +
708q GLU* 1.3 67.8 + - - +
760q SER* 6.0 2.9 - - - -
990q LEU* 4.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 708 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699q LYS* 5.9 4.5 - - + -
700q SER 3.3 10.1 - - - +
701q TYR* 4.4 1.8 - - - +
707q MET* 1.3 82.1 - - - +
709q SER* 1.3 66.7 + - - +
758q ARG 5.2 4.9 - - - +
759q THR* 5.8 0.4 - - - -
760q SER* 5.1 20.4 - - - +
990q LEU* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 709 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699q LYS* 4.6 1.8 - - - -
700q SER* 2.8 37.8 + - - +
708q GLU* 1.3 79.1 - - - +
710q LEU* 1.3 63.3 + - - +
711q THR* 3.7 3.2 + - - -
990q LEU 4.4 12.6 - - - -
991q VAL* 5.5 0.4 - - - -
992q LEU* 5.0 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 710 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697q LYS* 5.5 7.2 - - + -
698q GLN 3.4 13.7 - - - +
699q LYS* 4.4 3.6 - - + +
709q SER* 1.3 73.4 - - - +
711q THR* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 711 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697q LYS* 4.3 3.6 - - - -
698q GLN* 2.8 35.0 + - - +
700q SER* 5.6 6.7 - - - -
709q SER* 3.7 5.5 + - - -
710q LEU* 1.3 76.5 - - - +
712q VAL* 1.3 68.7 + - - +
713q THR* 3.5 4.1 + - - -
992q LEU 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 712 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617q THR* 5.0 13.7 - - - -
695q PHE* 5.1 7.6 - - + -
696q CYS 3.2 12.3 - - - +
697q LYS* 4.2 3.1 - - + +
711q THR* 1.3 77.5 - - - +
713q THR* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 713 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695q PHE* 3.4 5.4 - - - +
696q CYS* 2.8 33.2 + - - +
698q GLN* 4.8 11.4 - - - -
711q THR* 3.5 7.6 + - - -
712q VAL* 1.3 76.0 - - - +
714q PRO* 1.3 71.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 714 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694q GLY 3.3 11.4 - - - +
695q PHE* 4.5 0.7 - - + -
713q THR* 1.3 81.9 - - - +
715q CYS* 1.3 67.2 + - - +
748q LEU* 6.3 2.0 - - - -
----------------------------------------------------------
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