Contacts of the helix formed by residues 465 - 470 (chain T) 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 465 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461T SER 4.5 3.4 - - - +
462T ARG* 3.4 48.5 - - + +
463T ILE 3.2 0.6 - - - -
464T GLY* 1.3 79.0 - - - +
466T PHE* 1.3 59.1 + - - +
467T GLU 3.3 0.2 - - - -
468T SER* 3.0 21.3 + - - -
469T SER* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 466 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446T LEU* 5.1 8.1 - - + -
449T ALA* 5.9 1.1 - - + -
455T LEU* 3.5 46.0 - - + -
458T ILE* 5.4 9.4 - - + -
462T ARG 3.3 9.4 + - - +
463T ILE* 3.7 10.5 - - - +
464T GLY 3.2 0.4 - - - -
465T GLU* 1.3 73.8 - - - +
467T GLU* 1.3 62.4 + - - +
468T SER 3.0 2.7 - - - -
469T SER* 3.5 13.2 - - - -
470T PHE* 2.8 67.8 + + + +
503T THR* 5.7 2.9 - - - -
506T PHE* 3.9 36.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 467 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153T LYS* 2.7 40.8 + - - +
429T LEU* 3.8 13.2 - - + +
432T GLN* 5.5 0.3 - - - +
438T LEU* 3.3 26.7 - - + +
446T LEU* 3.8 30.7 - - + +
463T ILE 3.9 2.9 + - - +
464T GLY* 3.3 21.6 + - - +
465T GLU 3.3 0.2 - - - -
466T PHE* 1.3 79.5 - - - +
468T SER* 1.3 56.3 + - - +
470T PHE* 4.3 3.0 - - - +
471T LEU* 3.7 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 468 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464T GLY 3.9 3.2 + - - -
465T GLU* 3.0 26.3 + - - -
467T GLU* 1.3 77.5 - - - +
469T SER* 1.3 64.7 + - - +
470T PHE 3.3 2.0 - - - -
471T LEU* 3.7 14.2 - - - +
472T SER* 3.6 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 469 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462T ARG* 5.8 1.6 + - - -
465T GLU* 2.9 21.4 + - - +
466T PHE* 3.0 17.9 + - - -
468T SER* 1.3 79.2 + - - +
470T PHE* 1.3 58.9 + - - +
471T LEU 3.4 0.2 - - - -
472T SER* 4.0 6.0 + - - -
473T TYR* 3.8 15.2 + - - +
506T PHE* 4.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445T PRO* 4.7 22.9 - - + -
446T LEU* 6.1 4.7 - - + -
466T PHE* 2.8 45.3 + + + +
467T GLU* 4.8 3.1 - - - +
469T SER* 1.3 75.8 - - - +
471T LEU* 1.3 65.0 + - - +
472T SER 3.3 0.7 - - - -
473T TYR* 3.4 14.6 + + - +
474T LEU* 3.2 48.7 + - + +
481T LEU* 6.3 0.4 - - + -
499T LEU* 6.5 0.7 - - + -
502T ALA* 3.5 35.9 - - + -
503T THR* 5.3 6.1 - - + -
506T PHE* 3.7 22.2 - + - -
----------------------------------------------------------
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