Contacts of the helix formed by residues 399 - 403 (chain S) in PDB entry 5KZ5
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 GLU 399 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379S SER* 4.0 12.1 - - - +
381S CYS* 3.5 29.4 - - + -
393S ARG* 4.2 9.6 - - - +
398S ASP* 1.4 81.3 + - - +
400S ASP* 1.4 61.6 + - - +
402S ALA* 3.4 13.5 - - - +
403S HIS* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 400 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361S VAL 5.1 0.3 - - - +
363S GLY* 5.0 12.1 + - - -
398S ASP* 3.2 23.8 + - - +
399S GLU* 1.4 78.0 - - - +
401S LEU* 1.3 79.5 + - - +
403S HIS* 3.3 13.6 + - - +
404S SER* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358S PHE 4.0 2.9 - - - +
359S ALA* 4.1 14.6 - - + -
360S TYR* 3.7 26.9 - - - +
361S VAL 3.6 24.5 - - - +
362S GLU 5.8 0.4 - - - -
363S GLY* 6.1 0.2 - - - -
366S LEU* 4.2 13.5 - - + -
397S THR* 4.1 8.7 - - - -
398S ASP* 3.3 31.1 + - + +
400S ASP* 1.3 92.1 - - - +
402S ALA* 1.4 62.6 + - - +
404S SER* 3.2 7.6 + - - +
405S SER* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376S SER 5.3 0.2 - - - +
377S SER* 3.4 20.5 - - - -
379S SER* 4.9 5.2 - - - +
392S LEU* 3.5 23.3 - - + +
393S ARG* 3.8 18.4 - - - +
397S THR* 3.7 14.1 + - - +
398S ASP 3.0 12.8 + - - +
399S GLU* 3.4 12.1 - - - +
400S ASP 3.3 0.2 - - - -
401S LEU* 1.4 77.5 - - - +
403S HIS* 1.4 60.1 + - - +
404S SER 3.5 0.2 + - - -
405S SER* 3.6 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 403 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373S VAL* 5.1 2.4 - - - +
375S LEU* 3.6 37.1 - - + +
377S SER* 3.3 17.3 + - - -
379S SER* 3.4 23.8 + - - -
381S CYS* 3.9 16.5 - - + +
382S THR* 3.2 23.9 + - - -
399S GLU* 3.0 34.2 + - + +
400S ASP* 3.3 11.3 + - - +
402S ALA* 1.4 74.6 - - - +
404S SER* 1.4 57.6 + - - +
405S SER 3.4 7.8 + - - +
99e ILE* 5.7 3.2 - - + +
100e ALA* 6.1 2.5 - - + -
103e SER* 5.7 1.0 + - - -
----------------------------------------------------------
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