Contacts of the strand formed by residues 422 - 427 (chain C) in PDB entry 4K9N
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 VAL 422 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ILE* 3.3 11.7 - - + +
373C LEU* 3.4 30.7 - - + -
410C ALA* 3.6 24.7 - - + +
413C VAL* 3.8 13.9 - - + -
414C GLN* 2.9 47.4 + - + +
417C GLU 5.2 0.2 - - - +
420C ARG 3.7 7.2 - - - +
421C GLN* 1.3 88.2 + - - +
423C ILE* 1.3 64.3 + - - +
448C THR* 4.0 3.4 - - + -
449C ILE 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU* 4.0 20.0 - - + -
366C ALA* 3.8 28.7 - - + -
370C ALA* 4.4 7.4 - - + -
371C ILE 2.8 8.0 + - - +
372C TYR* 3.2 28.9 - - + +
373C LEU 3.0 20.5 + - - +
421C GLN* 4.1 17.0 - - + +
422C VAL* 1.3 79.7 - - - +
424C ALA* 1.3 61.1 + - - +
425C VAL* 3.8 8.0 + - + +
449C ILE* 3.3 15.5 - - + +
451C VAL* 3.9 26.0 - - + -
507C LEU* 6.0 1.1 - - + -
511C LEU* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LEU* 3.6 12.1 - - + +
406C ALA 4.2 3.4 - - - +
410C ALA* 3.7 27.4 - - + -
422C VAL* 4.1 0.8 - - - +
423C ILE* 1.3 71.6 - - - +
425C VAL* 1.3 58.0 + - - +
426C ILE* 3.8 23.9 + - + +
449C ILE 2.8 13.0 + - - +
450C PHE* 3.5 6.0 - - + -
451C VAL* 2.6 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C VAL* 5.5 0.2 - - + -
359C PHE* 4.0 17.0 - - + -
362C LEU* 4.0 26.2 - - + -
372C TYR* 5.0 1.1 - - + -
373C LEU 2.8 14.1 + - - +
374C ASN* 3.7 0.5 - - - -
375C GLU 2.8 25.5 + - - -
376C SER* 3.6 10.7 + - - -
383C MET* 4.1 19.7 - - + -
423C ILE* 4.4 10.1 - - + +
424C ALA* 1.3 73.4 - - - +
426C ILE* 1.3 63.4 + - - +
451C VAL* 3.5 9.0 - - + +
453C MET* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLU* 3.7 8.7 - - + +
376C SER* 4.4 3.1 - - - -
406C ALA* 4.1 10.5 - - + -
407C LEU* 3.6 48.7 - - + +
424C ALA* 3.8 21.8 - - + +
425C VAL* 1.3 80.5 - - - +
427C GLY* 1.3 74.9 + - - +
430C SER* 3.9 10.1 - - - +
431C ALA* 3.6 25.1 - - + +
450C PHE* 4.5 4.9 - - + -
451C VAL 2.9 9.3 + - - +
452C ILE* 3.3 13.3 - - + -
453C MET* 2.8 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLU 3.0 16.3 + - - -
376C SER* 3.9 4.3 - - - +
426C ILE* 1.3 75.3 - - - +
428C ASP* 1.3 60.4 + - - -
429C GLY 3.2 3.1 - - - -
430C SER 3.3 0.7 + - - -
431C ALA* 2.9 28.4 + - - +
452C ILE* 4.4 0.7 - - - -
453C MET* 3.6 13.9 - - - -
602C TZD 3.4 21.5 - - - -
----------------------------------------------------------
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