Contacts of the helix formed by residues 435 - 450 (chain A) in PDB entry 5JZU
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 HIS 435 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 5.7 5.4 - - + -
430A GLN* 2.7 39.2 + - + +
433A LEU* 3.9 35.2 + - + +
434A GLY* 1.3 74.3 - - - +
436A MET* 1.3 52.4 + - - +
437A ARG* 3.2 3.6 - - - -
438A GLY* 3.0 6.8 + - - +
439A SER* 2.7 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLN* 3.1 49.6 - - + +
434A GLY* 2.9 20.9 + - - +
435A HIS* 1.3 74.7 - - - +
437A ARG* 1.3 63.3 + - - +
439A SER* 3.3 5.7 + - - -
440A LEU* 3.0 24.8 + - - +
463A GLY* 5.1 2.4 - - - +
466A LEU* 4.2 33.7 - - + +
467A ILE* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A HIS 3.2 0.6 - - - -
436A MET* 1.3 77.9 - - - +
438A GLY* 1.3 62.2 + - - +
440A LEU* 3.3 21.3 + - - +
441A LEU* 3.6 13.3 + - - +
467A ILE* 4.5 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 4.8 0.7 + - - -
430A GLN* 3.5 16.4 + - - +
435A HIS* 3.0 12.6 + - - +
437A ARG* 1.3 77.4 - - - +
439A SER* 1.3 63.3 + - - +
440A LEU 3.1 2.1 + - - -
441A LEU* 3.4 13.9 + - - +
442A THR* 3.2 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 2.7 24.7 + - - -
430A GLN* 3.4 21.5 + - - -
431A GLN* 3.2 33.0 + - - +
435A HIS 2.7 19.4 + - - -
436A MET* 3.6 6.3 - - - -
438A GLY* 1.3 72.7 - - - +
440A LEU* 1.3 57.1 + - - +
441A LEU 3.5 0.2 - - - -
442A THR* 3.5 2.9 + - - -
443A LEU* 3.1 29.8 + - - +
463A GLY* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A MET 3.0 8.8 + - - +
437A ARG* 3.4 13.9 - - - +
438A GLY 3.1 0.4 - - - -
439A SER* 1.3 75.4 - - - +
441A LEU* 1.3 54.8 + - + +
443A LEU* 3.0 6.8 + - + +
444A GLN* 2.8 45.4 + - + +
460A LEU* 3.6 28.3 - - + -
463A GLY* 3.9 23.8 - - - +
464A TYR* 3.9 28.0 - - + +
467A ILE* 3.3 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG 3.6 12.3 + - - +
438A GLY* 3.4 12.2 + - - +
440A LEU* 1.3 79.3 - - + +
442A THR* 1.3 56.1 + - - +
444A GLN* 3.4 20.4 + - - +
445A ARG* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.5 37.6 - - + +
426A ARG* 2.8 27.6 + - + +
427A SER* 4.1 13.2 - - - +
430A GLN* 2.8 22.0 + - - +
438A GLY 3.2 3.9 + - - -
439A SER* 3.6 9.0 - - - -
440A LEU 3.1 0.2 - - - -
441A LEU* 1.3 80.0 - - - +
443A LEU* 1.3 56.9 + - - +
445A ARG* 3.3 9.1 + - + +
446A LEU* 3.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 6.2 1.1 - - + -
427A SER* 3.6 25.6 - - - +
431A GLN* 4.1 4.9 - - - +
439A SER* 3.1 26.4 + - - +
440A LEU* 3.0 8.1 + - - +
442A THR* 1.3 73.0 - - - +
444A GLN* 1.3 66.7 + - - +
446A LEU* 3.2 16.3 + - + +
447A VAL* 3.0 28.9 + - - +
456A LEU* 5.0 4.0 - - + +
459A ASP* 3.5 42.8 - - + +
460A LEU* 3.7 18.2 - - + +
463A GLY* 3.9 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 2.8 21.1 + - - +
441A LEU* 3.4 37.5 + - - +
443A LEU* 1.3 76.2 - - - +
445A ARG* 1.3 58.3 + - - +
447A VAL* 3.3 5.6 + - - +
448A GLN* 3.0 28.9 + - - +
460A LEU* 3.8 20.6 - - + -
464A TYR* 3.2 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN* 3.7 35.0 - - - +
409A ALA* 3.7 36.7 + - - +
410A SER* 4.8 2.2 - - - +
419A LEU* 5.8 0.2 - - - +
423A LEU* 4.3 14.5 - - + +
426A ARG* 5.9 0.6 - - - +
441A LEU 3.0 18.2 + - - +
442A THR* 3.4 8.7 - - - +
443A LEU 3.2 0.2 - - - -
444A GLN* 1.3 78.0 - - - +
446A LEU* 1.3 56.9 + - - +
448A GLN* 3.2 17.2 + - - +
449A LEU* 2.8 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 4.2 12.1 - - - +
423A LEU* 3.7 36.1 - - + +
424A LYS* 3.9 28.9 - - + +
427A SER* 5.1 0.2 - - - -
442A THR* 3.0 20.5 + - + +
443A LEU* 3.2 24.2 + - + +
445A ARG* 1.3 78.1 - - - +
447A VAL* 1.3 56.8 + - - +
449A LEU* 4.5 3.8 - - - -
450A PHE* 2.9 55.5 + - + +
456A LEU* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU 3.0 15.6 + - - +
444A GLN* 3.8 4.3 - - - +
445A ARG 3.2 0.2 - - - -
446A LEU* 1.3 75.0 - - - +
448A GLN* 1.3 64.5 + - - +
450A PHE 4.2 5.4 - - - +
451A PRO* 3.3 23.5 - - + +
456A LEU* 3.7 34.1 - - + +
457A LYS* 4.0 27.8 - - + +
460A LEU* 3.9 23.1 - - + -
479A GLU* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN 3.0 17.0 + - - +
445A ARG* 3.4 17.8 - - - +
447A VAL* 1.3 80.8 - - - +
449A LEU* 1.3 64.1 + - + +
451A PRO* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 4.3 21.1 - - + -
423A LEU* 3.7 23.1 - - + -
445A ARG* 2.8 48.0 + - + +
446A LEU* 3.9 1.3 - - - +
448A GLN* 1.3 81.5 - - + +
450A PHE* 1.3 84.2 + - + +
451A PRO* 3.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.7 38.8 - - + -
419A LEU* 3.8 23.1 - - + -
420A LYS* 3.8 39.3 - - + +
446A LEU* 2.9 27.8 + - + +
447A VAL* 3.4 9.3 - - - +
449A LEU* 1.3 94.8 - - + +
451A PRO* 1.3 60.1 - - - +
452A ASN 3.1 10.5 + - - -
453A ASP* 3.2 22.4 + - + +
456A LEU* 3.8 19.6 - - + +
----------------------------------------------------------
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