Contacts of the helix formed by residues 456 - 462 (chain F) in PDB entry 4E2I
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 ARG 456 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 3.7 12.1 - - - +
454E LEU 4.4 6.5 - - - +
455E ASP* 3.3 29.6 + - - +
456E ARG* 3.4 29.9 - - - +
458E ASN* 3.8 35.7 + - - +
459E PHE* 3.6 25.0 - - - -
510E GLU* 5.6 1.6 - - - -
452F LEU* 4.9 8.1 - - + -
453F PRO* 3.6 6.4 + - + +
455F ASP* 1.3 98.7 - - + +
457F LEU* 1.3 63.9 + - - +
458F ASN 3.1 2.9 - - - -
459F PHE* 3.0 36.8 + - + +
460F GLU* 3.1 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 4.7 8.7 - - + -
449F ASN 4.4 7.9 - - - +
450F VAL* 3.8 31.0 - - + -
452F LEU* 5.2 1.6 - - - +
453F PRO 3.5 6.1 + - - +
454F LEU* 3.6 33.2 - - + +
455F ASP 3.1 0.8 - - - -
456F ARG* 1.3 77.7 - - - +
458F ASN* 1.3 54.1 + - - +
460F GLU* 3.7 4.4 - - + +
461F LEU* 2.8 67.1 + - + +
493F ASN* 3.3 24.5 - - + +
497F LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 458 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 3.4 28.5 - - - +
456A ARG* 3.6 31.1 + - + +
459A PHE* 5.7 1.6 - - - +
460A GLU* 4.5 9.3 + - - +
454F LEU 3.6 12.8 - - - +
455F ASP 3.9 1.9 - - - +
456F ARG 3.1 0.6 - - - -
457F LEU* 1.3 78.8 - - - +
459F PHE* 1.3 65.0 + - + +
460F GLU 3.1 1.0 + - - -
461F LEU* 4.5 6.2 - - - +
462F GLY* 3.5 15.4 + - - -
500F TYR* 5.8 1.4 + - - -
510F GLU* 3.5 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 459 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ARG* 3.8 31.2 - - - -
459A PHE* 6.4 2.5 - + - -
458E ASN* 5.7 2.0 - - - +
459E PHE* 6.2 5.2 - + - -
510E GLU* 4.6 20.8 - - - +
515E ASN* 5.4 7.1 + - - +
455F ASP 4.0 11.4 - - - -
456F ARG* 3.0 27.8 + - + +
458F ASN* 1.3 77.4 - - + +
460F GLU* 1.3 57.5 + - - +
462F GLY* 4.4 3.2 + - - -
463F VAL* 4.6 7.1 - - - +
510F GLU* 3.7 25.6 - - - +
513F HIS* 5.6 13.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458E ASN* 4.1 17.6 + - - +
500E TYR* 4.3 13.0 + - - -
508E ASN* 4.0 23.1 - - + +
448F LEU* 3.2 19.4 - - + +
449F ASN* 2.7 50.5 + - - +
452F LEU* 4.4 11.6 - - - +
456F ARG 3.1 12.4 + - - +
457F LEU* 3.9 6.7 - - + +
458F ASN 3.1 0.2 - - - -
459F PHE* 1.3 79.3 - - - +
461F LEU* 1.3 58.0 - - + +
462F GLY 3.0 5.4 - - - -
463F VAL* 3.0 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 5.8 2.2 - - + -
448F LEU* 3.9 14.6 - - + -
449F ASN 6.0 0.7 - - - +
450F VAL* 5.1 0.2 - - + -
457F LEU* 2.8 58.6 + - + +
458F ASN* 4.5 5.8 - - - +
460F GLU* 1.3 71.8 - - + +
462F GLY* 1.3 56.8 + - - +
463F VAL 3.0 9.9 + - - -
464F ALA* 3.5 8.9 + - - +
472F PHE* 4.4 13.2 - - + -
497F LEU* 3.9 20.4 - - + -
500F TYR* 4.0 19.3 - - + +
509F LEU* 3.3 21.1 - - + +
521F PHE* 3.8 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458F ASN 3.5 9.2 + - - -
459F PHE 5.1 2.7 - - - -
460F GLU* 3.0 2.4 - - - +
461F LEU* 1.3 77.2 - - - +
463F VAL* 1.3 60.1 + - - +
464F ALA 3.5 0.7 - - - -
465F ILE* 3.0 33.4 - - - +
509F LEU* 4.3 6.3 - - - -
510F GLU 3.7 24.1 - - - +
511F LYS* 4.5 8.1 - - - +
----------------------------------------------------------
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