Contacts of the strand formed by residues 453 - 456 (chain C) in PDB entry 1IYH
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 453 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LYS 4.0 0.3 - - - +
406C LEU* 3.5 7.0 - - - +
407C THR* 3.1 52.5 + - + +
442C ILE* 5.3 2.9 - - + -
446C LEU* 4.2 32.3 - - + -
447C PRO* 6.5 0.4 - - + -
450C LYS 3.4 24.2 - - - +
451C ILE* 4.3 4.3 - - + -
452C PRO* 1.3 74.3 - - - +
454C LEU* 1.3 61.6 + - - +
455C GLU* 4.9 11.9 - - + +
460C THR* 4.2 18.4 - - + -
461C LEU 3.2 14.8 - - - +
462C HIS* 4.1 11.2 - - + -
467C ILE* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C TYR* 4.0 10.5 - - + -
405C LYS 3.6 28.9 - - - +
406C LEU* 4.0 13.2 - - + +
418C ILE* 5.0 0.4 - - + -
422C PHE* 4.0 28.0 - - + -
453C ILE* 1.3 75.3 - - - +
455C GLU* 1.3 61.8 + - - +
456C VAL* 3.7 22.3 + - + -
459C LEU 3.5 1.2 - - - +
460C THR* 4.5 0.9 - - - -
461C LEU* 2.7 45.5 + - + +
467C ILE* 3.5 38.5 - - + +
471C LEU* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASN 3.4 5.6 - - - +
404C TYR* 3.4 2.8 - - - -
405C LYS* 2.9 67.7 + - + +
407C THR* 4.5 7.0 + - - +
453C ILE* 4.9 12.0 - - + +
454C LEU* 1.3 74.1 - - - +
456C VAL* 1.3 61.0 + - - +
457C ASP 4.0 0.7 - - - -
458C GLY* 4.9 14.2 - - - +
459C LEU 3.2 8.7 - - - +
460C THR* 4.1 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 4.8 7.9 - - - -
402C PRO* 4.4 5.2 - - + -
403C ASN 3.7 2.5 - - - -
404C TYR* 3.7 36.1 - - + -
454C LEU* 3.9 6.5 - - + -
455C GLU* 1.3 75.0 - - - +
457C ASP* 1.3 82.7 + - + +
459C LEU* 2.6 30.6 + - - +
461C LEU* 3.6 32.3 - - + -
470C TYR* 4.0 18.6 - - + +
----------------------------------------------------------
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