Contacts of the helix formed by residues 424 - 431 (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 CYS 424 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.0 20.1 - - + +
389A LEU* 4.9 1.4 - - + +
404A ILE* 4.2 20.2 - - + -
408A THR* 5.5 0.7 - - - -
419A LEU* 3.1 44.3 + - + +
420A VAL* 3.7 8.6 + - - -
422A LEU 3.8 0.4 - - - -
423A GLY* 1.3 76.0 - - - +
425A ILE* 1.3 66.8 + - - +
427A PRO* 3.5 8.7 - - - +
428A LEU* 3.4 24.5 + - - +
450A ILE* 4.1 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 3.9 31.2 + - + +
423A GLY 3.3 1.8 - - - -
424A CYS* 1.3 76.9 - - - +
426A LYS* 1.3 64.9 + - - +
428A LEU* 3.2 7.6 + - - +
429A CYS* 2.9 31.5 + - - -
447A LEU* 4.3 4.0 - - + -
450A ILE* 4.4 16.4 - - + -
468A TYR* 4.3 15.7 - - + -
471A LEU* 3.7 38.6 - - + +
472A ILE* 3.7 31.9 - - + -
475A ALA* 4.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 5.5 4.7 - - - +
423A GLY 4.0 3.2 + - - +
425A ILE* 1.3 77.6 - - - +
427A PRO* 1.4 67.5 - - + +
429A CYS* 3.0 3.1 + - - +
430A ASP* 2.8 57.1 + - - +
474A GLU 5.4 0.6 + - - -
475A ALA* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.4 10.3 - - + +
389A LEU* 3.4 33.9 - - + +
390A GLN* 4.0 30.3 - - + +
397A ARG* 4.9 0.6 + - - +
423A GLY 3.1 21.5 - - - +
424A CYS* 3.5 10.8 - - - +
426A LYS* 1.4 96.6 - - + +
428A LEU* 1.3 60.6 + - - +
430A ASP* 3.5 11.5 + - + +
431A LEU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 3.8 21.5 - - + -
401A ALA* 4.8 4.7 - - - +
404A ILE* 4.3 24.0 - - + -
405A THR* 4.3 14.4 - - - +
408A THR* 5.2 0.7 - - + -
424A CYS* 3.4 17.6 + - - +
425A ILE 3.2 4.4 + - - +
426A LYS 3.2 0.4 - - - -
427A PRO* 1.3 79.9 - - - +
429A CYS* 1.3 62.9 + - - +
431A LEU* 3.3 27.3 + - + +
432A LEU* 3.8 3.6 + - - +
443A ALA* 3.5 28.0 - - - +
446A GLY* 4.4 11.2 - - - -
447A LEU* 4.1 15.7 - - + +
450A ILE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 2.9 25.8 + - - +
426A LYS 3.0 7.8 + - - +
428A LEU* 1.3 74.9 - - - +
430A ASP* 1.3 59.8 + - - +
432A LEU* 2.9 35.1 + - - +
433A THR* 4.2 2.1 + - - +
447A LEU* 3.9 19.3 - - - -
472A ILE* 4.2 9.2 - - - -
475A ALA* 3.7 33.2 - - + +
476A TYR* 4.1 26.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 5.8 3.1 - - - +
397A ARG* 4.5 12.9 + - - +
426A LYS* 2.8 56.7 + - - +
427A PRO* 3.6 10.3 - - + +
429A CYS* 1.3 77.0 - - - +
431A LEU* 1.3 56.4 + - - +
432A LEU 3.2 0.2 - - - -
433A THR* 2.9 26.4 + - - -
434A VAL* 4.2 6.6 - - - +
475A ALA 4.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 3.5 27.6 - - + -
394A PHE* 6.1 0.2 - - + -
397A ARG* 3.8 28.0 - - + +
401A ALA* 3.9 17.7 - - + -
427A PRO 3.2 14.7 + - - +
428A LEU* 3.5 14.6 - - + +
429A CYS 3.1 1.2 - - - -
430A ASP* 1.3 70.7 - - - +
432A LEU* 1.3 64.2 + - - +
433A THR 3.1 4.2 + - - -
434A VAL* 3.3 24.9 + - + +
439A ILE* 3.3 33.5 - - + +
440A VAL* 3.5 13.9 - - - +
443A ALA* 3.8 17.5 - - + -
----------------------------------------------------------
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