Contacts of the helix formed by residues 425 - 437 (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 ASP 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 3.7 12.3 - - + -
422A GLU* 2.7 27.1 + - - +
424A SER* 1.3 86.0 + - - +
426A LYS* 1.3 61.1 + - - -
427A ARG 3.2 3.0 + - - -
428A SER* 3.3 13.4 + - - +
429A PHE* 3.0 26.1 + - + +
408B GLY* 2.7 39.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
421A VAL* 3.6 16.6 - - + -
422A GLU 3.2 11.6 + - - +
423A GLU* 2.6 44.1 + - - +
425A ASP* 1.3 77.6 - - - +
427A ARG* 1.3 63.1 + - - +
429A PHE* 4.3 0.2 - - - -
430A LEU* 2.9 24.4 + - - +
515A PHE* 3.0 57.3 + - + +
516A ASP* 3.1 16.7 + - - +
517A LEU 5.2 0.2 - - - +
543A PHE* 3.8 26.2 + - + -
545A ASN* 3.6 14.5 - - - +
548A ASN* 5.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU 4.8 1.7 + - - +
424A SER 4.9 3.6 + - - +
425A ASP 3.2 1.2 + - - -
426A LYS* 1.3 77.1 - - + +
428A SER* 1.3 60.6 + - - +
430A LEU* 3.3 5.7 + - - +
431A LEU* 3.2 23.9 + - - +
455A SER* 2.4 40.0 + - - -
456A LEU* 4.2 12.9 - - + +
459A PHE* 3.7 54.5 - - + +
515A PHE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A SER 5.3 1.7 + - - -
425A ASP* 3.3 17.3 + - - +
427A ARG* 1.3 73.7 - - - +
429A PHE* 1.3 61.3 + - - +
431A LEU* 3.2 16.5 + - - +
432A ASP* 3.0 36.7 + - - -
459A PHE* 4.8 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 3.8 24.0 - - + -
420A TRP 4.5 1.1 - - - -
421A VAL* 3.7 26.5 - - + -
425A ASP* 3.0 21.7 + - + +
426A LYS 3.8 2.0 - - - +
428A SER* 1.3 76.8 + - - +
430A LEU* 1.3 57.4 + - - +
432A ASP* 3.4 8.9 + - - +
433A LEU* 2.8 29.0 + - + +
543A PHE* 3.6 29.8 - + - -
413B ASN* 4.1 15.7 - - - -
534B VAL* 3.4 28.3 - - + -
535B GLY* 3.7 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS 2.9 19.1 + - - +
427A ARG 3.5 5.2 - - - +
428A SER 3.2 0.2 - - - -
429A PHE* 1.3 76.9 - - - +
431A LEU* 1.3 56.4 + - - +
433A LEU* 3.2 2.3 + - + +
434A LEU* 2.9 41.1 + - + +
445A VAL* 4.5 11.2 - - + -
456A LEU* 4.0 37.9 - - + -
459A PHE* 5.7 0.2 - - + -
460A LEU* 4.1 21.5 - - + -
513A ILE* 3.8 41.7 - - + -
515A PHE* 4.2 4.5 - - + -
543A PHE* 4.2 12.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
427A ARG 3.5 10.8 - - - +
428A SER* 3.2 15.1 + - - +
430A LEU* 1.3 76.9 - - - +
432A ASP* 1.3 64.2 + - - +
434A LEU* 3.3 3.8 + - + +
435A ASN* 3.1 30.4 + - - +
459A PHE* 3.7 24.0 - - + -
460A LEU* 3.9 18.4 - - + -
463A GLU* 3.8 24.5 - - + +
465A TYR* 3.3 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A SER* 3.0 24.4 + - - +
429A PHE* 3.8 5.3 - - - +
431A LEU* 1.3 76.2 - - - +
433A LEU* 1.3 57.3 + - - +
435A ASN* 3.5 7.8 + - - +
436A ALA* 2.9 31.0 + - - +
534B VAL* 3.4 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PHE* 2.8 21.9 + - + +
430A LEU* 3.6 4.7 - - + +
432A ASP* 1.3 70.9 - - - +
434A LEU* 1.3 57.4 + - - +
436A ALA* 4.1 3.8 - - + -
437A THR* 2.7 58.5 + - - +
511A HIS* 4.1 7.4 - - + -
513A ILE* 3.8 24.0 - - + -
541A THR* 3.9 19.7 - - + +
543A PHE* 3.8 29.8 - - + -
534B VAL* 3.9 9.6 - - + +
535B GLY* 3.5 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 2.9 42.0 + - + +
431A LEU* 3.3 5.1 + - - +
433A LEU* 1.3 79.1 - - - +
435A ASN* 1.3 64.0 + - - +
437A THR* 3.5 16.3 + - - -
439A LYS 4.4 6.6 + - - +
443A THR* 3.8 31.2 - - + +
445A VAL* 5.3 0.4 - - + -
460A LEU* 4.1 16.2 - - + -
465A TYR* 4.1 20.9 - - + -
493A ILE* 3.7 33.2 - - + -
511A HIS* 5.9 0.9 - - - +
513A ILE* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.1 14.2 + - - +
432A ASP* 3.7 8.6 - - - +
434A LEU* 1.3 78.8 - - - +
436A ALA* 1.3 61.2 + - - +
437A THR 4.4 2.8 - - - -
465A TYR* 2.5 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ASP 2.9 20.0 + - - +
433A LEU 3.5 4.7 - - - +
435A ASN* 1.3 76.3 - - - +
437A THR* 1.3 65.1 + - - +
533B ARG* 3.8 33.9 + - + +
534B VAL* 4.0 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 2.7 46.7 + - - +
434A LEU* 3.5 9.4 + - - -
435A ASN 3.4 3.7 - - - -
436A ALA* 1.3 78.6 - - - +
439A LYS* 3.3 57.1 + - + +
511A HIS* 3.5 30.3 - - + +
539A LEU* 3.9 11.0 - - + -
533B ARG* 5.1 3.9 - - - +
----------------------------------------------------------
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