Contacts of the strand formed by residues 406 - 412 (chain F) in PDB entry 1K9V
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 406 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F LEU* 2.9 34.8 + - + +
391F PHE* 3.2 43.4 - - + -
392F GLU* 4.0 4.8 + - - +
404F SER 3.2 2.4 - - - -
405F LEU* 1.3 86.9 - - - +
407F GLU* 1.3 71.3 + - - +
408F GLY 3.2 3.5 + - - +
451F HIS* 3.9 29.6 - - + -
467F VAL* 4.2 17.3 - - + -
468F ARG 4.8 0.2 - - - -
469F LYS* 4.1 20.9 - - + +
472F ILE* 3.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F PHE* 3.8 1.3 - - - -
392F GLU* 3.4 13.2 - - - +
406F ILE* 1.3 72.1 - - - +
408F GLY* 1.3 58.4 + - - +
447F CYS* 3.7 20.4 - - - +
448F GLU* 4.6 4.3 + - + -
451F HIS* 3.0 33.3 + - + +
469F LYS* 2.6 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F PHE* 3.2 10.9 - - - +
392F GLU* 3.0 39.8 + - - +
406F ILE 3.2 0.6 + - - -
407F GLU* 1.3 74.1 - - - +
409F ASN* 1.3 61.9 + - - -
446F VAL 3.2 14.4 - - - -
447F CYS* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F PHE* 4.2 1.1 - - - -
392F GLU* 5.5 0.2 - - + -
393F GLU* 3.5 36.4 - - + +
395F GLU* 5.4 0.8 - - - +
408F GLY* 1.3 77.0 - - - +
410F VAL* 1.3 65.9 + - - +
411F VAL* 3.3 31.7 - - - +
445F ALA* 3.5 4.0 - - - +
446F VAL* 2.8 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F PHE* 4.3 2.2 - - + -
388F GLN* 3.7 48.2 - - + +
391F PHE* 4.2 7.6 - - + -
393F GLU 2.8 19.8 + - - +
394F SER* 3.2 15.9 - - - +
395F GLU* 3.0 28.5 + - - +
409F ASN* 1.3 80.8 + - - +
411F VAL* 1.3 64.5 + - - +
443F TYR* 3.5 25.1 - - + -
444F ARG 3.2 16.2 - - - +
445F ALA* 4.4 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F GLU* 3.6 27.8 - - + +
409F ASN* 3.3 27.6 - - - +
410F VAL* 1.3 74.8 - - - +
412F LYS* 1.3 67.4 + - - +
443F TYR* 3.3 5.8 - - - -
444F ARG* 2.8 46.6 + - + +
446F VAL* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F GLU* 3.5 10.6 + - - +
411F VAL* 1.3 84.3 - - - +
413F LEU* 1.3 77.6 + - - +
414F ARG* 3.5 5.4 + - - -
418F LEU* 3.4 21.2 - - + +
442F THR* 3.5 20.4 - - + +
443F TYR* 3.2 39.8 - - + -
444F ARG* 4.5 0.9 - - - +
461F GLU* 4.6 1.4 - - - +
----------------------------------------------------------
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