Contacts of the helix formed by residues 454 - 458 (chain X) in PDB entry 3FKS
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 GLU 454 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401T GLU* 5.2 2.1 - - - +
402T VAL* 5.6 4.2 - - - +
405X GLU* 5.1 2.1 - - - +
408X ARG* 3.2 50.2 + - + +
409X LYS* 4.2 27.0 - - + +
412X ARG* 3.9 28.9 + - - -
452X ILE 3.7 0.2 + - - -
453X PRO* 1.3 69.1 - - - +
455X HIS* 1.3 64.7 + - - +
456X ALA 3.0 5.6 + - - -
457X PHE* 3.2 18.4 + - - +
458X TYR 4.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 455 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395T PHE* 5.0 15.5 - + - -
398T GLN* 4.4 32.6 - - + +
416T THR* 5.7 9.2 - - + -
412X ARG* 5.7 2.0 - - - +
453X PRO* 3.5 4.3 - - + +
454X GLU* 1.3 77.9 - - - +
456X ALA* 1.3 62.3 + - - +
457X PHE 3.3 0.2 - - - -
458X TYR* 3.2 26.0 + + + +
469X LYS* 3.5 27.5 + - - -
473X LEU* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 456 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452X ILE* 3.6 20.2 - - + -
453X PRO* 3.4 21.7 + - + +
454X GLU 3.0 0.4 + - - -
455X HIS* 1.3 80.6 - - - +
457X PHE* 1.3 61.2 + - - +
458X TYR 3.1 1.3 + - - -
460X VAL* 3.9 10.4 - - - +
466X VAL* 3.8 18.8 - - + +
469X LYS* 3.8 20.6 - - - +
470X ALA* 4.3 17.5 - - + -
473X LEU* 4.5 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 457 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409X LYS* 3.5 55.4 - - + +
412X ARG* 3.0 16.3 - - + +
413X PHE* 3.4 37.3 - + + +
415X SER 4.6 0.5 - - - +
444X VAL* 4.0 29.4 - - + -
449X TYR* 4.0 24.9 - - + -
452X ILE* 3.8 14.4 - - + -
453X PRO 3.5 18.6 - - - -
454X GLU 3.2 9.6 + - - +
456X ALA* 1.3 76.9 - - - +
458X TYR* 1.3 59.6 + - - +
459X MET 3.6 1.0 + - - -
460X VAL* 3.7 6.2 + - - +
463X ILE* 4.7 3.8 - - + -
466X VAL* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 458 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394T LEU* 3.6 32.4 - - + +
398T GLN* 3.1 45.7 + - + +
343X GLY 2.7 26.7 + - - -
344X ILE* 4.0 7.9 - - + -
412X ARG* 3.9 22.0 - - + +
415X SER* 3.7 16.8 - - - -
427X ILE* 5.4 3.1 - - + -
454X GLU 4.2 0.6 + - - -
455X HIS* 3.4 26.6 - + + +
456X ALA 3.1 2.8 - - - -
457X PHE* 1.3 77.3 - - - +
459X MET* 1.3 84.8 + - + +
460X VAL* 3.5 3.5 + - - +
469X LYS* 2.8 34.3 + - - -
----------------------------------------------------------
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