Contacts of the strand formed by residues 689 - 693 (chain F) in PDB entry 6T8O
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 ILE 689 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404F PRO* 5.8 7.4 - - + -
446F ASP* 3.4 29.4 - - - +
452F ILE* 4.9 5.8 - - + -
679F LEU* 4.5 0.9 - - - -
680F TYR* 2.8 46.3 + - + +
682F PRO* 4.7 9.0 - - + -
687F LEU* 3.5 20.9 - - + +
688F PRO* 1.3 74.5 - - - +
690F ARG* 1.3 63.9 + - - +
691F VAL* 3.3 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 690 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F ILE* 3.4 32.7 - - - +
367F ARG* 6.2 0.2 - - - +
398F ARG* 3.8 26.0 - - - +
412F GLU* 3.1 31.6 + - - +
446F ASP* 3.8 20.4 - - - +
447F ILE* 4.0 24.5 + - + +
671F GLN 5.2 1.8 + - - -
672F LEU* 3.5 18.8 - - + +
673F LEU* 3.6 16.0 - - - +
677F ASP* 2.4 38.6 + - - +
678F MET 3.5 13.0 - - - +
679F LEU* 3.8 12.7 - - + +
688F PRO 3.9 3.0 + - - -
689F ILE* 1.3 72.3 - - - +
691F VAL* 1.3 61.8 - - - +
692F HIS* 4.0 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 691 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443F LEU* 3.9 37.7 - - + +
444F GLY 4.0 4.7 - - - +
445F HIS 3.4 11.4 - - - +
446F ASP* 4.3 1.3 - - - +
452F ILE* 4.0 24.2 - - + -
677F ASP* 3.7 2.0 - - - +
678F MET* 2.8 48.2 + - + +
680F TYR* 3.8 16.2 - - + -
689F ILE* 3.3 19.0 + - + +
690F ARG* 1.3 75.9 - - - +
692F HIS* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 692 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F PRO* 5.1 6.3 - - + +
364F VAL* 3.5 44.7 + - + +
365F ILE* 4.2 15.2 - - + +
418F ARG* 5.3 2.1 + - - +
421F VAL* 3.7 22.7 - - + +
443F LEU 4.0 0.9 - - - -
444F GLY* 3.3 22.0 - - - -
445F HIS* 3.2 12.0 + - + +
446F ASP 3.4 26.7 + - - -
447F ILE* 4.3 7.3 - - - +
676F GLY 3.4 6.5 + - - +
677F ASP* 3.2 26.4 + - - +
690F ARG* 4.0 15.2 - - - +
691F VAL* 1.3 71.5 - - - +
693F GLY* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 693 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421F VAL* 3.8 5.7 - - - +
443F LEU 3.4 8.5 - - - -
474F VAL* 6.1 0.4 - - - -
475F GLY* 6.2 2.7 - - - -
652F PHE* 5.5 0.2 - - - -
676F GLY* 2.4 29.7 + - - +
678F MET* 3.8 18.5 - - - +
691F VAL 3.8 2.6 + - - -
692F HIS* 1.3 67.3 - - - +
694F ALA* 1.3 62.2 + - - -
695F PHE 3.4 0.2 + - - -
801F ADP 2.8 26.9 + - - -
----------------------------------------------------------
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