Contacts of the helix formed by residues 449 - 463 (chain A) in PDB entry 2JGN
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 THR 449 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 3.6 2.7 - - - +
448A GLU* 1.3 95.2 - - + +
450A LYS* 1.3 58.4 + - - +
451A LYS* 3.5 19.7 + - - +
452A GLY* 3.1 22.3 + - - +
453A ALA 2.9 24.6 + - - -
497A THR* 3.5 11.2 - - - +
516A ASP* 4.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A THR* 1.3 74.0 - - - +
451A LYS* 1.3 62.1 + - - +
453A ALA 3.3 0.5 + - - -
454A ASP* 3.0 18.7 + - - +
471A HIS* 3.4 62.4 + - + +
497A THR* 2.9 30.9 + - + -
498A ALA* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A THR* 3.3 18.2 + - - +
450A LYS* 1.3 78.5 - - - +
452A GLY* 1.3 56.7 + - - +
454A ASP* 3.4 7.0 + - + +
455A SER* 2.8 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 4.1 9.6 - - - +
449A THR* 3.1 21.0 + - - -
451A LYS* 1.3 76.4 - - - +
453A ALA* 1.3 58.6 + - - +
455A SER* 4.2 4.8 + - - -
456A LEU* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 3.6 12.0 - - + +
449A THR 2.9 11.2 + - - +
450A LYS 3.3 8.7 + - - +
452A GLY* 1.3 75.5 - - - +
454A ASP* 1.3 64.9 + - - +
456A LEU* 3.8 0.7 - - - -
457A GLU* 3.0 24.3 + - - +
469A SER* 4.3 7.4 - - - -
471A HIS* 3.6 23.6 - - + +
495A VAL* 3.7 28.4 - - + +
497A THR* 4.0 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LYS 3.0 12.7 + - - +
451A LYS* 3.5 8.1 - - + +
453A ALA* 1.3 81.3 - - - +
455A SER* 1.3 65.2 + - - +
457A GLU* 3.2 14.7 + - - +
458A ASP* 3.2 22.2 + - - +
469A SER* 4.9 0.2 - - - -
471A HIS* 3.3 22.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 2.4 33.6 + - - -
451A LYS* 2.8 25.1 + - - -
452A GLY* 4.2 5.0 + - - -
454A ASP* 1.3 75.9 - - - +
456A LEU* 1.3 56.6 + - - +
458A ASP* 3.2 7.8 + - - +
459A PHE* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 4.2 13.0 - - + +
430A LEU* 4.0 17.9 - - + -
445A VAL* 3.9 14.8 - - + -
447A VAL* 3.8 25.1 - - + -
452A GLY 2.9 19.6 + - - +
453A ALA 3.9 3.1 - - - +
455A SER* 1.3 78.6 + - - +
457A GLU* 1.3 56.8 + - - +
459A PHE* 3.3 24.6 + - + +
460A LEU* 2.9 36.9 + - + +
495A VAL* 4.3 9.9 - - + -
515A PHE* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ALA 3.0 12.1 + - - +
454A ASP* 3.2 15.0 + - - +
456A LEU* 1.3 76.7 - - - +
458A ASP* 1.3 58.2 + - - +
460A LEU* 3.4 2.1 + - - -
461A TYR* 2.9 28.9 + - + +
467A CYS* 3.6 27.4 - - - +
468A THR* 3.7 19.1 - - - +
469A SER* 2.5 36.8 + - - -
495A VAL* 4.8 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ASP* 3.2 11.4 + - - +
455A SER* 3.5 11.0 - - - +
456A LEU 3.2 0.6 - - - -
457A GLU* 1.3 78.7 - - - +
459A PHE* 1.3 64.8 + - - +
461A TYR* 3.2 10.0 + - - +
462A HIS* 3.0 59.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 3.7 64.8 - - + +
428A SER* 4.8 1.6 - - - -
430A LEU* 5.7 0.7 - - + -
431A LEU* 3.7 32.3 - - + -
455A SER 2.9 14.0 + - - +
456A LEU* 3.5 23.8 - - + +
458A ASP* 1.3 75.9 - - - +
460A LEU* 1.3 62.4 + - + +
462A HIS* 3.2 7.3 + - + +
463A GLU* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.1 15.5 - - + -
431A LEU* 3.9 27.6 - - + -
434A LEU* 4.1 16.4 - - + -
456A LEU* 2.9 30.3 + - + +
459A PHE* 1.3 78.6 - - + +
461A TYR* 1.3 59.9 + - - +
463A GLU* 3.3 5.4 + - - +
464A GLY 3.2 4.2 + - - -
465A TYR* 2.9 38.6 + - + +
467A CYS* 3.6 25.1 - - + -
493A ILE* 4.3 15.9 - - + -
495A VAL* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU* 2.9 19.8 + - + +
458A ASP* 3.2 11.2 + - - +
460A LEU* 1.3 76.3 - - - +
462A HIS* 1.3 88.7 + + - +
464A GLY* 2.9 20.3 + - - -
465A TYR 3.9 10.3 - - - -
466A ALA* 6.5 0.2 - - - -
467A CYS* 4.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ASP* 3.0 43.9 + - - +
459A PHE* 3.2 6.8 + - + +
461A TYR* 1.3 98.2 - + - +
463A GLU* 1.3 63.2 + - - +
464A GLY 3.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.8 30.1 - - + +
459A PHE* 2.9 37.4 + - + +
460A LEU* 3.5 10.8 - - - +
461A TYR 3.2 0.2 - - - -
462A HIS* 1.3 82.3 - - - +
464A GLY* 1.3 56.9 + - - +
465A TYR* 3.5 22.1 - - + -
----------------------------------------------------------
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