Contacts of the helix formed by residues 430 - 442 (chain A) in PDB entry 4L28
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 430 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR 3.7 2.1 + - - -
429A ILE* 1.3 76.9 - - - +
431A CYS* 1.3 62.2 + - - +
433A HIS* 3.3 30.2 - - + +
434A THR* 2.9 24.3 + - - -
475A PRO 2.8 25.3 + - - +
476A SER* 3.0 22.3 + - - -
477A ASP 3.0 7.7 + - - -
478A GLN* 4.6 1.6 - - - +
479A VAL* 3.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 1.3 78.8 + - - +
432A GLY* 1.3 58.2 + - - +
434A THR* 3.1 5.2 + - - -
435A ILE* 2.9 34.4 + - + +
464A MET* 3.9 27.9 - - + +
468A LEU* 5.4 4.7 - - + -
473A VAL* 4.1 20.2 - - + -
474A GLN 4.0 6.7 - - - +
475A PRO* 3.7 9.4 - - + +
477A ASP 3.0 15.2 + - - +
478A GLN 3.8 13.5 - - - -
479A VAL* 4.0 9.4 - - - -
482A VAL* 5.1 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A CYS* 1.3 77.9 - - - +
433A HIS* 1.3 59.5 + - - +
435A ILE* 3.2 15.2 + - - +
436A GLU* 2.9 39.1 + - - +
468A LEU* 5.7 0.2 - - - -
475A PRO* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.7 22.8 - - + +
430A THR* 3.3 32.1 + - + +
432A GLY* 1.3 77.0 - - - +
434A THR* 1.3 56.7 + - - +
436A GLU* 3.1 16.7 + - - +
437A ILE* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 4.2 24.2 - - + -
429A ILE* 3.3 24.5 - - - +
430A THR 2.9 13.1 + - - -
431A CYS 3.1 7.2 + - - -
433A HIS* 1.3 75.5 + - - +
435A ILE* 1.3 67.1 + - - +
437A ILE* 3.8 8.2 - - + +
438A LEU* 2.9 44.2 + - + +
446A ALA* 5.1 2.5 - - + -
459A VAL* 5.3 3.4 - - + -
464A MET* 3.7 19.3 - - + -
479A VAL* 3.6 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A CYS* 2.9 18.2 + - + +
432A GLY* 3.4 15.7 - - - +
433A HIS 3.2 0.2 - - - -
434A THR* 1.3 76.2 - - - +
436A GLU* 1.3 68.6 + - + +
438A LEU* 3.9 1.5 - - - +
439A ARG* 2.9 56.3 + - - +
461A LEU* 3.9 18.2 - - + -
464A MET* 3.9 23.1 - - + -
465A LEU* 4.0 13.7 - - + -
468A LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY 2.9 20.9 + - - +
433A HIS* 3.1 16.7 + - - +
435A ILE* 1.3 82.0 - - + +
437A ILE* 1.3 58.0 + - + +
439A ARG* 3.9 5.4 - - - +
440A GLU* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.6 29.8 - - + -
425A VAL* 5.8 6.3 - - + -
429A ILE* 5.0 5.4 - - + -
433A HIS* 2.9 45.7 + - + +
434A THR* 3.2 8.5 + - + +
436A GLU* 1.3 75.5 - - + +
438A LEU* 1.3 63.1 + - + +
440A GLU* 3.3 11.9 + - - +
441A LYS* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 5.3 9.0 - - + +
425A VAL* 6.1 0.7 - - + -
434A THR* 2.9 36.9 + - + +
435A ILE* 4.0 2.9 - - - +
437A ILE* 1.3 77.6 - - + +
439A ARG* 1.3 62.8 + - - +
441A LYS* 3.3 1.6 + - + +
442A GLY 2.9 6.8 + - - -
443A PHE* 2.9 61.2 + - + +
444A ASN 4.4 4.5 - - - +
445A GLN* 3.7 35.9 - - - +
446A ALA* 4.0 11.2 - - + +
459A VAL* 4.9 3.4 - - + +
460A THR 5.1 0.4 - - - -
461A LEU* 4.5 20.6 - - + +
464A MET* 5.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE* 2.9 38.6 + - - +
436A GLU* 3.9 5.4 - - - +
438A LEU* 1.3 76.5 - - - +
440A GLU* 1.3 63.7 + - - +
442A GLY* 3.1 13.8 + - - +
443A PHE 4.8 1.6 - - - -
461A LEU* 4.2 21.4 - - + +
465A LEU* 4.1 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLU* 2.9 22.7 + - - +
437A ILE* 3.6 11.9 - - - +
439A ARG* 1.3 78.0 - - - +
441A LYS* 1.3 68.7 + - + +
442A GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.1 24.7 - - + -
437A ILE* 2.9 21.5 + - + +
438A LEU* 4.0 2.7 - - + +
440A GLU* 1.3 85.3 - - + +
442A GLY* 1.3 59.1 + - - +
443A PHE* 3.2 34.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU 2.9 5.8 + - - -
439A ARG* 3.1 12.1 + - - -
440A GLU 3.4 0.4 - - - -
441A LYS* 1.3 78.0 - - - +
443A PHE* 1.3 63.4 + - - +
444A ASN* 4.1 0.3 + - - +
----------------------------------------------------------
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