Contacts of the helix formed by residues 458 - 470 (chain C) in PDB entry 4PE5
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 PHE 458 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C PRO 4.4 2.0 - - - +
408C PHE* 2.7 46.0 + + + +
457C GLY* 1.3 68.7 - - - -
459C CYS* 1.3 62.6 + - - +
460C ILE 3.2 0.3 + - - -
461C ASP* 3.3 5.3 + - - +
462C LEU* 2.9 35.8 + - + +
533C PHE* 3.6 41.5 - + - -
534C LYS* 4.8 10.8 - - + -
785C MET* 4.2 17.9 - - + -
788C LEU* 3.5 50.9 - - + +
789C ASP* 4.4 5.2 - - + -
792C TRP* 4.3 17.7 - + + -
793C VAL* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 3.4 26.7 + - - -
409C VAL* 3.8 13.0 - - + -
458C PHE* 1.3 85.7 - - - +
460C ILE* 1.3 59.6 + - + +
462C LEU* 4.2 7.4 - - - -
463C LEU* 2.9 28.8 + - - +
514C VAL* 3.3 26.9 - - + +
515C ALA* 3.7 27.4 - - - -
516C PRO* 3.8 5.6 - - - -
533C PHE* 4.6 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C THR* 5.2 4.5 - - + -
408C PHE 5.1 0.7 - - - +
409C VAL* 4.9 12.3 - - + -
432C LYS* 4.5 10.1 - - + +
433C LYS* 4.8 0.9 - - - -
434C VAL* 3.7 29.4 - - + +
455C CYS* 3.7 28.7 - - + +
456C TYR* 3.6 25.6 - - - +
457C GLY* 3.6 13.2 + - - +
458C PHE 3.1 0.6 - - - -
459C CYS* 1.3 80.1 - - + +
461C ASP* 1.3 65.5 + - - +
463C LEU* 3.2 12.7 + - + +
464C ILE* 2.9 27.9 + - + +
476C VAL* 4.8 8.3 - - + -
514C VAL 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C VAL* 5.3 2.4 - - - +
432C LYS* 4.4 17.8 + - - +
457C GLY 2.8 21.4 + - - +
458C PHE 3.8 3.1 - - - +
460C ILE* 1.3 82.9 - - - +
462C LEU* 1.3 57.4 + - - +
464C ILE* 3.2 8.8 + - - +
465C LYS* 2.9 27.2 + - - +
784C PHE* 5.1 2.3 - - + -
788C LEU* 4.2 21.4 - - + +
792C TRP* 3.5 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C PHE* 2.9 23.1 + - + +
459C CYS* 3.8 6.3 - - - +
461C ASP* 1.3 75.1 - - - +
463C LEU* 1.3 59.2 + - - +
465C LYS* 3.1 11.9 + - + +
466C LEU* 2.9 42.8 + - + +
514C VAL* 5.1 7.6 - - + -
533C PHE* 3.7 46.0 - - + -
760C ILE* 4.5 5.8 - - + -
776C ILE* 3.7 17.3 - - + -
779C SER* 5.2 2.7 - - - +
784C PHE* 5.1 2.0 - - + -
785C MET* 3.7 24.0 - - + -
788C LEU* 4.8 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ILE* 3.7 40.6 - - + -
434C VAL* 5.5 0.9 - - + -
459C CYS 2.9 20.5 + - - +
460C ILE* 3.2 14.1 + - + +
462C LEU* 1.3 76.8 - - - +
464C ILE* 1.3 56.8 + - - +
466C LEU* 3.4 10.4 + - + +
467C ALA* 2.9 29.7 + - + +
474C TYR* 4.0 21.5 - - + -
476C VAL* 3.7 31.2 - - + -
512C MET* 5.2 2.7 - - - -
514C VAL* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LYS* 5.0 21.8 - - + -
460C ILE* 2.9 14.9 + - + +
461C ASP* 3.2 13.7 + - - +
463C LEU* 1.3 76.7 - - - +
465C LYS* 1.3 57.3 + - - +
467C ALA* 3.5 6.8 + - - +
468C ARG* 2.9 28.4 + - - +
474C TYR* 4.9 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ASP 2.9 13.0 + - - +
462C LEU* 3.1 14.3 + - + +
464C ILE* 1.3 75.6 - - - +
466C LEU* 1.3 62.7 + - + +
468C ARG* 3.1 7.6 + - - +
469C THR* 2.9 33.8 + - - +
775C SER* 5.4 0.7 - - - +
779C SER* 5.8 2.9 - - - +
784C PHE* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LEU* 2.9 33.1 + - + +
463C LEU* 3.8 11.9 - - + +
465C LYS* 1.3 77.5 - - + +
467C ALA* 1.3 58.7 + - - +
469C THR* 4.0 2.8 - - - +
470C MET* 3.0 32.7 + - - +
512C MET* 4.9 9.4 - - - -
514C VAL* 5.1 4.7 - - + -
760C ILE* 4.4 14.4 - - + -
772C VAL* 4.0 33.9 - - + -
775C SER* 3.3 32.3 - - - +
776C ILE* 4.1 15.5 - - + -
779C SER* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C LEU* 2.9 20.2 + - + +
464C ILE* 3.8 5.2 - - - +
465C LYS 3.2 0.2 - - - -
466C LEU* 1.3 75.7 - - - +
468C ARG* 1.3 62.9 + - - +
470C MET 3.0 19.5 - - - +
471C GLN* 3.7 7.6 - - - -
472C PHE 4.0 10.2 + - - +
474C TYR* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ILE 2.9 17.6 + - - +
465C LYS* 3.1 9.4 + - - +
467C ALA* 1.3 77.4 - - - +
469C THR* 1.3 66.1 + - - +
471C GLN* 4.7 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LYS* 2.9 15.9 + - - +
466C LEU* 4.0 3.1 - - - -
468C ARG* 1.3 80.9 - - - +
470C MET* 1.3 64.1 + - + +
471C GLN* 3.5 3.1 + - - +
775C SER* 3.7 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C LEU 3.0 17.1 + - - +
467C ALA* 3.0 13.4 - - - +
469C THR* 1.3 77.4 - - + +
471C GLN* 1.3 60.4 + - - +
472C PHE* 2.9 13.7 + - - +
768C TRP* 4.3 24.0 - - + -
771C GLN* 5.6 12.1 - - + +
----------------------------------------------------------
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