Contacts of the strand formed by residues 716 - 722 (chain C) in PDB entry 6DBT
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 LEU 716 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C ASP* 3.3 31.9 - - + +
605C SER* 4.9 4.3 - - - -
607C CYS* 4.7 1.6 - - - -
608C THR* 5.4 7.2 - - + -
711C ILE 3.4 1.0 - - - +
712C SER* 4.2 0.7 - - - -
713C VAL 2.8 31.6 + - - +
714C GLY 3.1 6.1 - - - +
715C GLY* 1.3 83.5 - - - +
717C LEU* 1.3 64.8 + - - +
718C ARG* 3.3 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 717 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C THR* 4.4 10.9 - - - +
710C ILE* 4.2 27.1 - - + +
711C ILE 3.4 6.5 - - - +
712C SER* 4.1 17.3 - - - +
715C GLY 4.4 9.4 - - - +
716C LEU* 1.3 73.4 - - - +
718C ARG* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 718 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C ILE* 4.3 5.9 - - - +
594C MET* 3.0 35.3 - - - +
597C LEU* 5.1 5.1 - - - +
607C CYS* 3.4 31.7 + - - +
608C THR* 3.4 14.1 - - + +
611C PHE* 4.7 11.1 - - + -
709C LEU 3.4 0.9 - - - +
710C ILE* 3.2 10.5 - - - -
711C ILE 2.9 32.9 + - - +
713C VAL* 3.0 45.6 + - - +
714C GLY 3.9 4.8 + - - -
716C LEU* 3.3 39.4 - - + +
717C LEU* 1.3 78.6 - - - +
719C SER* 1.3 63.8 + - - +
720C PHE* 3.9 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 719 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C THR 2.8 14.8 + - - -
609C SER* 2.8 28.6 + - - +
611C PHE* 3.4 19.6 - - - +
708C ARG* 3.4 29.0 + - - +
709C LEU 3.1 7.8 + - - -
710C ILE* 3.7 9.6 - - - -
718C ARG* 1.3 73.9 - - - +
720C PHE* 1.3 76.3 + - - +
721C ARG* 5.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 720 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C LEU* 3.6 35.2 - - + -
593C ILE* 5.1 10.8 - - + -
611C PHE* 3.5 43.7 - + + -
613C VAL* 4.8 5.2 - - + -
649C ILE* 4.7 6.3 - - + -
707C SER 4.6 0.3 - - - +
708C ARG* 3.4 8.7 - - - +
709C LEU* 2.9 45.0 + - + +
711C ILE* 4.0 31.0 - - + -
713C VAL* 4.9 10.1 - - + -
718C ARG* 3.9 20.4 - - + -
719C SER* 1.3 88.0 + - - +
721C ARG* 1.3 62.8 + - - +
722C PHE* 4.2 13.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 721 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C SER 5.7 3.4 - - - +
610C GLY* 6.5 0.9 - - - -
611C PHE 3.0 14.8 + - - +
612C THR* 4.4 13.1 + - + +
613C VAL 3.3 16.2 + - - -
705C MET 4.6 11.3 + - - +
706C GLU* 3.6 13.5 + - - +
707C SER 5.2 3.6 - - - -
708C ARG* 3.5 40.8 - - + +
719C SER* 5.0 3.1 - - - +
720C PHE* 1.3 76.6 - - - +
722C PHE* 1.3 81.3 + - - +
723C PHE* 4.8 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 722 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C TRP* 5.1 4.7 - + - -
582C LEU* 3.5 39.9 - - + -
586C LEU* 3.9 17.7 - - + -
612C THR* 5.0 0.7 - - - -
613C VAL* 3.4 38.8 - - + +
615C VAL* 4.6 6.5 - - + -
704C MET* 4.7 20.6 + - + +
705C MET* 4.0 23.2 + - - +
707C SER 5.7 2.0 - - - -
709C LEU* 4.1 25.1 - - + -
720C PHE* 4.2 11.4 - - + -
721C ARG* 1.3 98.7 + - - +
723C PHE* 1.3 80.2 + - - +
724C PHE* 4.3 14.6 - + + -
----------------------------------------------------------
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