Contacts of the helix formed by residues 424 - 432 (chain E) in PDB entry 3KHU
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 424 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E TYR* 2.9 21.7 + - + +
422E GLU 3.8 0.8 + - - -
423E LEU* 1.3 68.7 - - - +
425E TYR* 1.3 58.2 + - - +
426E GLU* 3.4 12.1 + - - +
427E ARG* 3.3 36.9 + - + +
428E ILE* 3.1 28.5 + - - +
606E EDO 5.0 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 425 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E LEU* 4.9 1.4 - - - +
411E VAL* 5.3 8.7 - - + -
413E ILE* 4.1 8.5 - - - +
420E PHE 2.7 29.7 + - - -
421E LYS 4.5 0.9 - - - -
423E LEU* 3.1 42.1 + - + +
424E ASP* 1.3 69.2 + - - +
426E GLU* 1.3 61.1 + - - +
427E ARG 3.2 0.2 - - - -
428E ILE* 3.9 21.1 - - + -
429E HIS* 2.9 29.6 + - - +
438E ILE* 3.9 29.4 - - + -
445E LEU* 3.8 26.8 - - + +
448E LEU* 5.2 0.9 - - + -
452E LEU* 3.6 22.9 - - + -
455E ILE* 4.3 2.9 - - + -
457E PHE* 3.5 14.2 - + + -
606E EDO 3.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E ASP* 3.3 9.9 + - - +
425E TYR* 1.3 75.8 - - - +
427E ARG* 1.3 63.4 + - - +
429E HIS* 3.2 4.7 + - - +
430E LYS* 3.2 44.3 + - - +
455E ILE* 4.0 35.4 - - + +
606E EDO 4.8 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E ASP* 5.4 0.2 + - - -
402E TYR* 3.5 59.2 - - + +
424E ASP* 3.3 29.5 + - - +
426E GLU* 1.3 80.6 - - - +
428E ILE* 1.3 62.8 + - - +
430E LYS* 3.4 23.3 + - - +
431E LYS* 3.7 10.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E LEU* 6.0 0.2 - - + -
401E PRO 5.5 0.4 - - - +
402E TYR* 3.7 28.5 - - + -
405E CYS* 3.7 33.8 - - + +
411E VAL* 4.4 3.6 - - + -
423E LEU* 4.2 16.6 - - + -
424E ASP 3.1 15.3 + - - +
425E TYR* 3.7 31.2 - - + +
426E GLU 3.3 0.2 - - - -
427E ARG* 1.3 75.5 - - - +
429E HIS* 1.3 67.6 + - - +
431E LYS* 3.3 5.5 + - - +
432E MET* 3.2 41.2 + - - +
457E PHE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E TYR 2.9 14.0 + - - +
426E GLU 3.4 10.1 - - - +
428E ILE* 1.3 76.5 - - - +
430E LYS* 1.3 63.1 + - - +
432E MET* 3.1 11.4 + - - +
434E LYS* 2.9 44.1 + - + +
436E ALA* 4.8 3.7 - - + +
455E ILE* 2.7 48.3 + - + -
456E GLY* 3.3 24.4 + - - -
457E PHE* 3.8 18.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 430 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E GLU* 3.2 33.9 + - - +
427E ARG* 3.7 13.4 - - - +
428E ILE 3.3 0.6 - - - -
429E HIS* 1.3 79.2 - - - +
431E LYS* 1.3 64.1 + - + +
432E MET 4.3 0.2 - - - +
434E LYS* 3.5 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E CYS 4.6 0.4 - - - -
406E ASP* 3.1 44.2 + - - +
407E GLY* 2.8 29.4 + - - +
427E ARG* 3.7 8.2 + - + +
428E ILE* 3.3 7.7 + - - +
429E HIS 3.2 0.6 - - - -
430E LYS* 1.3 84.5 - - + +
432E MET* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 432 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E CYS 3.5 14.4 - - - +
408E ALA* 3.3 27.8 - - + +
409E HIS 3.4 25.4 - - - +
410E ALA* 3.5 10.5 - - - +
411E VAL* 3.6 15.5 - - + -
428E ILE* 3.2 32.5 + - + +
429E HIS 3.1 10.7 + - - +
431E LYS* 1.3 79.9 - - - +
433E LEU* 1.3 64.6 + - - +
434E LYS* 2.7 29.3 + - - -
436E ALA* 4.0 13.2 - - + -
437E PHE 3.8 10.3 - - - +
457E PHE* 3.7 16.6 - - - -
----------------------------------------------------------
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