Contacts of the helix formed by residues 472 - 480 (chain B) in PDB entry 5WJ9
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 ASP 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE* 3.3 26.0 - - + +
475A VAL* 4.3 12.0 - - - +
453B LYS* 2.8 34.4 + - + +
463B CYS* 6.1 0.2 - - - -
466B SER* 5.2 0.4 - - - +
467B LEU* 4.0 1.3 - - + +
471B ASP* 1.3 86.8 - - - +
473B MET* 1.3 60.3 + - - +
474B PHE 3.5 0.7 - - - -
475B VAL* 3.8 17.2 - - + +
476B THR* 3.3 27.3 + - + +
471C ASP* 3.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LEU* 4.4 20.9 - - + +
470B GLY* 4.7 11.2 - - - -
471B ASP 3.1 1.9 - - - -
472B ASP* 1.3 76.6 - - - +
474B PHE* 1.3 59.4 + - - +
476B THR* 2.7 21.1 + - - +
477B PHE* 3.1 27.6 - - + -
502B ILE* 3.4 34.1 - - + -
506B ILE* 4.6 4.0 - - - -
465C PHE* 3.4 31.2 - - + +
466C SER* 3.6 16.2 - - - +
469C ASN* 3.4 31.6 - - - +
471C ASP* 2.9 16.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B MET* 1.3 78.1 - - - +
475B VAL* 1.3 59.0 + - + +
476B THR 3.3 0.4 - - - -
477B PHE* 3.3 6.5 + - - +
478B ALA* 2.8 42.0 + - + -
481B GLN* 6.4 1.1 - - + -
453C LYS* 3.5 38.4 - - + -
459C MET* 3.9 11.7 - - + -
462C GLU* 4.0 16.2 - - + -
463C CYS* 3.6 47.1 - - + -
466C SER* 3.6 17.7 - - - +
471C ASP* 3.4 3.6 + - - +
472C ASP* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 3.7 25.4 - - - +
472B ASP* 3.7 23.1 + - + +
473B MET 3.5 0.4 - - - -
474B PHE* 1.3 77.1 - - + +
476B THR* 1.3 53.6 + - - +
478B ALA* 3.1 10.0 + - + +
479B ALA* 2.8 33.8 + - + +
472C ASP* 4.3 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 3.5 12.8 - - + +
454B PHE* 4.8 9.0 - - + -
463B CYS* 3.5 31.6 - - - -
467B LEU* 3.8 11.1 - - + +
472B ASP 3.3 14.3 + - - +
473B MET* 2.7 27.5 + - - +
475B VAL* 1.3 77.7 - - - +
477B PHE* 1.3 61.6 + - - -
479B ALA* 3.4 19.5 + - - +
480B MET* 3.6 15.6 - - - +
498B LEU* 3.6 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B MET* 3.1 46.9 - - + -
474B PHE* 3.3 8.9 + - + +
476B THR* 1.3 82.2 + - - +
478B ALA* 1.3 56.9 + - - +
480B MET* 3.2 25.0 + - - +
481B GLN* 3.4 14.2 + - - -
495B GLN* 3.5 24.0 - - - -
498B LEU* 3.3 43.1 - - + -
499B TYR* 3.9 33.4 - + - -
502B ILE* 5.5 0.9 - - + -
462C GLU* 3.5 41.4 - - + +
465C PHE* 4.3 5.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PHE* 2.8 39.6 + - + +
475B VAL* 3.1 14.8 + - + +
477B PHE* 1.3 69.5 - - - +
479B ALA* 1.3 66.1 + - - +
480B MET 3.2 0.7 - - - -
481B GLN* 3.4 24.5 + - + +
482B ALA 4.5 1.0 + - - -
462C GLU* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HIS* 3.2 36.9 + - + +
452B VAL* 5.3 7.0 - - + +
453B LYS* 6.2 3.8 - - + +
475B VAL* 2.8 12.6 + - + +
476B THR* 3.4 14.8 - - - +
478B ALA* 1.3 78.2 - - - +
480B MET* 1.3 59.7 + - + +
481B GLN 3.4 0.7 + - - -
482B ALA* 3.7 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 4.2 11.2 - - + -
451B HIS* 2.9 48.7 - - + +
454B PHE* 5.0 6.1 - - + -
476B THR 3.6 20.6 - - - +
477B PHE* 3.3 15.7 - - - +
478B ALA 3.2 1.4 - - - -
479B ALA* 1.3 74.3 - - + +
481B GLN* 1.3 59.5 + - - +
482B ALA 3.2 1.3 - - - -
483B GLN* 2.8 20.7 + - - +
484B GLN 3.1 10.9 + - - -
490B VAL 5.1 0.2 - - - +
491B TRP* 3.5 25.3 - - + +
494B SER* 2.9 36.3 - - - +
495B GLN* 4.1 8.7 - - - +
498B LEU* 4.3 13.2 - - + -
----------------------------------------------------------
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