Contacts of the helix formed by residues 467 - 477 (chain A) in PDB entry 2JDQ
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 PRO 467 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLY* 3.4 14.1 - - - +
457A GLU* 4.3 18.8 - - + -
458A ALA 4.8 0.7 - - - +
465A ILE* 3.5 11.6 - - + +
466A ASN* 1.3 90.7 - - - +
468A TYR* 1.3 83.0 + - + +
469A CYS 3.3 0.9 + - - -
470A ALA* 4.0 6.6 + - - +
471A LEU* 3.9 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA 4.6 0.2 + - - -
416A ILE* 4.0 15.5 - - + +
417A LYS* 3.7 28.6 + - + +
420A VAL* 3.8 24.7 - - + -
425A ILE* 4.3 4.5 - - + -
450A ILE* 3.2 46.0 - - + -
451A LEU* 4.3 9.6 - - + -
453A LEU* 4.5 2.4 - - + +
454A GLY* 3.7 25.6 - - - -
457A GLU* 4.3 12.4 + - + +
466A ASN* 3.1 6.0 + - - +
467A PRO* 1.3 91.3 - - + +
469A CYS* 1.3 59.4 + - - +
470A ALA 3.5 0.2 - - - -
471A LEU* 3.8 20.4 - - + -
472A ILE* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 4.0 16.6 - - - -
455A GLU* 5.7 0.2 - - - -
465A ILE* 6.1 0.7 - - + -
466A ASN* 3.6 32.5 - - - +
467A PRO 3.3 0.2 - - - -
468A TYR* 1.3 76.0 - - - +
470A ALA* 1.3 61.1 + - - +
472A ILE* 3.4 3.5 + - - +
473A GLU* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ASN 4.5 1.8 + - - +
467A PRO 4.0 7.7 + - - +
469A CYS* 1.3 79.4 - - - +
471A LEU* 1.3 59.2 + - + +
473A GLU* 3.4 11.0 + - - +
474A GLU* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 3.7 30.7 - - + -
425A ILE* 3.7 22.0 - - + +
467A PRO* 3.9 9.8 + - + +
468A TYR* 3.6 17.3 + - + +
469A CYS 3.2 0.6 - - - -
470A ALA* 1.3 76.1 - - + +
472A ILE* 1.3 60.8 + - - +
474A GLU* 3.3 12.0 + - + +
475A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 3.7 26.9 - - + -
429A CYS* 4.2 11.9 - - - -
432A LEU* 6.4 0.2 - - + -
447A LEU* 4.0 26.2 - - + +
450A ILE* 5.3 2.2 - - + -
451A LEU* 3.6 37.7 - - + -
468A TYR* 3.0 26.0 + - + +
469A CYS* 3.9 4.3 - - - +
471A LEU* 1.3 74.5 - - - +
473A GLU* 1.3 57.9 + - - +
475A ALA* 3.2 0.7 + - - +
476A TYR* 2.8 39.5 + - + +
481A ILE* 4.3 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A CYS* 2.9 23.1 + - - +
470A ALA* 3.6 9.1 - - - +
472A ILE* 1.3 76.7 - - - +
474A GLU* 1.3 58.8 + - - +
477A GLY* 2.9 31.0 + - - -
478A LEU* 2.6 38.1 + - + +
481A ILE* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS* 5.4 0.7 + - - -
470A ALA* 2.9 22.0 + - + +
471A LEU* 3.3 15.9 + - + +
473A GLU* 1.3 76.0 - - - +
475A ALA* 1.3 62.1 + - - +
477A GLY* 4.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 4.1 4.5 - - + -
426A LYS* 2.9 58.0 + - + +
429A CYS* 3.7 25.4 - - + +
430A ASP* 4.4 0.7 - - - +
471A LEU 3.0 16.2 + - - +
472A ILE 3.2 0.4 + - - +
474A GLU* 1.3 78.3 - - - +
476A TYR* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A CYS* 4.1 19.7 - - + -
432A LEU* 3.7 46.8 + - + +
433A THR* 4.5 8.4 - - + +
472A ILE* 2.8 18.9 + - + +
475A ALA* 1.3 81.0 - - - +
477A GLY* 1.3 59.1 + - - +
480A LYS* 3.6 56.1 + - + +
481A ILE* 3.8 21.5 - - + -
484A LEU* 3.8 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU 2.9 16.1 + - - -
474A GLU 5.0 2.5 - - - -
475A ALA 3.7 0.8 - - - -
476A TYR* 1.3 80.3 - - - +
478A LEU* 1.3 61.4 + - - -
479A ASP* 3.2 7.4 - - - -
480A LYS* 3.3 4.2 + - - -
481A ILE* 3.0 30.2 + - - +
----------------------------------------------------------
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